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# Download
SeqKit is implemented in [Go](https://golang.org/) programming language,
statically-linked executable binary files are [freely available](https://github.com/shenwei356/seqkit/releases).
Please cite:
1. Wei Shen\*, Botond Sipos, and Liuyang Zhao. 2024. SeqKit2: A Swiss Army Knife for Sequence and Alignment Processing. ***iMeta*** e191. [doi:10.1002/imt2.191](https://doi.org/10.1002/imt2.191).
<span class="__dimensions_badge_embed__" data-doi="10.1002/imt2.191" data-style="small_rectangle"></span>
2. Wei Shen, Shuai Le, Yan Li\*, and Fuquan Hu\*. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation.
***PLOS ONE***. [doi:10.1371/journal.pone.0163962](https://doi.org/10.1371/journal.pone.0163962).
<span class="__dimensions_badge_embed__" data-doi="10.1371/journal.pone.0163962" data-style="small_rectangle"></span>
## Current Version
- [SeqKit v2.9.0](https://github.com/shenwei356/seqkit/releases/tag/v2.9.0) - 2024-11-01
[](https://github.com/shenwei356/seqkit/releases/tag/v2.9.0)
- `seqkit`:
- **Fix sequence ID parsing with the default regular expression (in this case, we actually use bytes.Index instead) for a rare case: "xxx\tyyy zzz" was wrongly parsed as "xxx\tyyy"**. [#486](https://github.com/shenwei356/seqkit/issues/486)
- `seqkit locate`:
- **Fix `-G/--non-greedy` for tandem repeats**, e.g., ATTCGATTCGATTCG (ATTCGx3).
- `seqkit grep/subseq`:
- Fix negative regions longer than sequence length. [#479](https://github.com/shenwei356/seqkit/issues/479).
- `seqkit stats`:
- Add an extra column `sum_n` to count the number of ambiguous characters. [#490](https://github.com/shenwei356/seqkit/issues/490)
### Links
OS |Arch |File, 中国镜像 |Download Count
:------|:---------|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Linux |32-bit |[seqkit_linux_386.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/seqkit_linux_386.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_linux_386.tar.gz) |[](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/seqkit_linux_386.tar.gz)
Linux |**64-bit**|[**seqkit_linux_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/seqkit_linux_amd64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_linux_amd64.tar.gz) |[](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/seqkit_linux_amd64.tar.gz)
Linux |**arm64** |[**seqkit_linux_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/seqkit_linux_arm64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_linux_arm64.tar.gz) |[](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/seqkit_linux_arm64.tar.gz)
macOS |**64-bit**|[**seqkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/seqkit_darwin_amd64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_darwin_amd64.tar.gz) |[](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/seqkit_darwin_amd64.tar.gz)
macOS |**arm64** |[**seqkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/seqkit_darwin_arm64.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_darwin_arm64.tar.gz) |[](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/seqkit_darwin_arm64.tar.gz)
Windows|32-bit |[seqkit_windows_386.exe.tar.gz](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/seqkit_windows_386.exe.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_windows_386.exe.tar.gz) |[](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/seqkit_windows_386.exe.tar.gz)
Windows|**64-bit**|[**seqkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/seqkit_windows_amd64.exe.tar.gz), <br/> [中国镜像](http://app.shenwei.me/data/seqkit/seqkit_windows_amd64.exe.tar.gz)|[](https://github.com/shenwei356/seqkit/releases/download/v2.9.0/seqkit_windows_amd64.exe.tar.gz)
*Notes*
- please open an issuse to request binaries for other platforms.
- run `seqkit version` to check update !!!
- run `seqkit genautocomplete` to update shell autocompletion script !!!
## Installation
#### Method 1: Download binaries (latest stable version)
Just [download](https://github.com/shenwei356/seqkit/releases) compressed
executable file of your operating system,
and decompress it with `tar -zxvf *.tar.gz` command or other tools.
And then:
1. **For Linux-like systems**
1. If you have root privilege simply copy it to `/usr/local/bin`:
sudo cp seqkit /usr/local/bin/
1. Or copy to anywhere in the environment variable `PATH`:
mkdir -p $HOME/bin/; cp seqkit $HOME/bin/
1. **For windows**, just copy `seqkit.exe` to `C:\WINDOWS\system32`.
#### Method 2: Install via conda (latest stable version) [](https://anaconda.org/bioconda/seqkit) [](https://anaconda.org/bioconda/seqkit)
conda install -c bioconda seqkit
#### Method 3: Install via [homebrew](https://brew.sh/) (might not be latest stable version)
brew install seqkit
#### Method 4: For Go developer (latest stable/dev version)
go get -u github.com/shenwei356/seqkit/v2/seqkit/
#### Method 5: Docker based installation (might not be latest stable versio)
[Install Docker](https://docs.docker.com/engine/installation/#supported-platforms)
git clone this repo:
git clone https://github.com/shenwei356/seqkit
Run the following commands:
cd seqkit
docker build -t shenwei356/seqkit .
docker run -it shenwei356/seqkit:latest
#### Method 6: Compiling from source (latest stable/dev version)
# ------------------- install golang -----------------
# download Go from https://go.dev/dl
wget https://go.dev/dl/go1.17.13.linux-amd64.tar.gz
tar -zxf go1.17.13.linux-amd64.tar.gz -C $HOME/
# or
# echo "export PATH=$PATH:$HOME/go/bin" >> ~/.bashrc
# source ~/.bashrc
export PATH=$PATH:$HOME/go/bin
# ------------- the latest stable version -------------
go get -v -u github.com/shenwei356/seqkit/seqkit
# The executable binary file is located in:
# ~/go/bin/seqkit
# You can also move it to anywhere in the $PATH
mkdir -p $HOME/bin
cp ~/go/bin/seqkit $HOME/bin/
# --------------- the development version --------------
git clone https://github.com/shenwei356/seqkit
cd seqkit/seqkit/
go build
# The executable binary file is located in:
# ./seqkit
# You can also move it to anywhere in the $PATH
mkdir -p $HOME/bin
cp ./seqkit $HOME/bin/
## Shell-completion
Supported shell: bash|zsh|fish|powershell
Bash:
# generate completion shell
seqkit genautocomplete --shell bash
# configure if never did.
# install bash-completion if the "complete" command is not found.
echo "for bcfile in ~/.bash_completion.d/* ; do source \$bcfile; done" >> ~/.bash_completion
echo "source ~/.bash_completion" >> ~/.bashrc
Zsh:
# generate completion shell
seqkit genautocomplete --shell zsh --file ~/.zfunc/_seqkit
# configure if never did
echo 'fpath=( ~/.zfunc "${fpath[@]}" )' >> ~/.zshrc
echo "autoload -U compinit; compinit" >> ~/.zshrc
fish:
seqkit genautocomplete --shell fish --file ~/.config/fish/completions/seqkit.fish
## Release history
- [SeqKit v2.8.2](https://github.com/shenwei356/seqkit/releases/tag/v2.8.2) - 2024-05-17
[](https://github.com/shenwei356/seqkit/releases/tag/v2.8.2)
- `seqkit amplicon`:
- Fix a big introduced in v2.7.0. When more than one pairs of primers are given, only the last one is used. [#457](https://github.com/shenwei356/seqkit/issues/457)
- `seqkit translate`:
- Add option `-e/--skip-translate-errors` to skip translate error and output empty sequence. [#458](https://github.com/shenwei356/seqkit/pull/458)
- `seqkit split`:
- Add flag `-I/--ignore-case` for `-i/--by-id`. [#462](https://github.com/shenwei356/seqkit/issues/462)
- [SeqKit v2.8.1](https://github.com/shenwei356/seqkit/releases/tag/v2.8.1) - 2024-04-07
[](https://github.com/shenwei356/seqkit/releases/tag/v2.8.1)
- `seqkit sana`:
- Add support for FASTQ files with IDs in the separator (`+`, 3rd) lines.. [#446](https://github.com/shenwei356/seqkit/pull/446), [#429](https://github.com/shenwei356/seqkit/issues/429), [#408](https://github.com/shenwei356/seqkit/issues/408)
- `seqkit subseq`:
- Add some docs to show how to keep the original order of sequences when extracting with BED: compress the input FASTA file. [#451](https://github.com/shenwei356/seqkit/issues/451)
- [SeqKit v2.8.0](https://github.com/shenwei356/seqkit/releases/tag/v2.8.0) - 2024-03-11
[](https://github.com/shenwei356/seqkit/releases/tag/v2.8.0)
- `seqkit stats`:
- Add column `N50_num`, an alias of L50, [#15](https://github.com/shenwei356/seqkit/issues/15).
- `seqkit seq/locate/fish/watch`:
- Removing the flag `-V/--validate-seq-length`. Now the whole sequence will be checked if `-v/--validate-seq` is given.
- `seqkit amplicon`:
- Fix the speed problem, introduced in v2.7.0. [#439](https://github.com/shenwei356/seqkit/issues/439).
- Slightly faster by reusing objects.
- `seqkit seq`:
- Change the threshold sequence length for parallelizing complement sequence computation, 1kb->1Mb.
- [SeqKit v2.7.0](https://github.com/shenwei356/seqkit/releases/tag/v2.7.0) - 2024-01-31
[](https://github.com/shenwei356/seqkit/releases/tag/v2.7.0)
- `seqkit`:
- Grouping subcommands in help message, which is intuitive for beginners.
- `seqkit grep`:
- New flag: `-D/--allow-duplicated-patterns` for outputting records multiple times when duplicated patterns are given. [#427](https://github.com/shenwei356/seqkit/issues/427)
- `seqkit subseq`:
- Use the ID regular expression from the option `--id-regexp` to create FASTA index file. This solves the panic happened for sequences containing tabs in the headers. [#432](https://github.com/shenwei356/seqkit/issues/432)
- `seqkit split/sort/shuffle`:
- When using the two-pass mode (`-2/--two-pass`), replace possible tabs in the sequence header.
- `seqkit rmdup`:
- Write an empty file of duplicate numbers and lists of IDs even if there's no duplicates when using `-D/--dup-num-file`. [#436](https://github.com/shenwei356/seqkit/issues/436)
- `seqkit stats`:
- New flag `-S/--skip-file-check` to skip input file checking when given files or a file list. It's very useful if you run it with millions of files.
- [SeqKit v2.6.1](https://github.com/shenwei356/seqkit/releases/tag/v2.6.1) - 2023-11-18
[](https://github.com/shenwei356/seqkit/releases/tag/v2.6.1)
- `seqkit`:
- fix panic of nil pointer introduced in v2.6.0, which happens when handling multiple input files and some of them have file sizes of zero.
- `seqkit seq`:
- fix panic (close of closed channel) when using `-v` to checking sequences.
- [SeqKit v2.6.0](https://github.com/shenwei356/seqkit/releases/tag/v2.6.0) - 2023-11-09
[](https://github.com/shenwei356/seqkit/releases/tag/v2.6.0)
- `seqkit`:
- add the shortcut `-X` for the flag `--infile-list`.
- `seqkit common`:
- **add a new flag `-e/--check-embedded-seqs` for detecting embedded sequences.**
- for matching by sequences: reduced the memory occupation and corrected numbers in the log. [#416](https://github.com/shenwei356/seqkit/issues/416)
- `seqkit stat`:
- add a new column `AvgQual` for average quality score. [#411](https://github.com/shenwei356/seqkit/issues/411)
- `seqkit split2`:
- fix the panic for invalid input.
- `seqkit subseq`:
- add a new flag `-R/--region-coord` for appending coordinates to sequence ID for `-r/--region`. [#413](https://github.com/shenwei356/seqkit/issues/413)
- `seqkit locate`:
- add a new flag `-s/--max-len-to-show` to show at most X characters for the search pattern or matched sequences.
- `seqkit seq`:
- change the nucleotide color theme. [#412](https://github.com/shenwei356/seqkit/pull/412)
- [SeqKit v2.5.1](https://github.com/shenwei356/seqkit/releases/tag/v2.5.1) - 2023-08-09
[](https://github.com/shenwei356/seqkit/releases/tag/v2.5.1)
- `seqkit stats`:
- **fix a concurrency bug (file name error) introduced in v2.5.0**. [#405](https://github.com/shenwei356/seqkit/issues/405)
- `seqkit subseq`:
- sequence/chromosome IDs are case-sensitive now. [#400](https://github.com/shenwei356/seqkit/issues/400)
- [SeqKit v2.5.0](https://github.com/shenwei356/seqkit/releases/tag/v2.5.0) - 2023-07-16
[](https://github.com/shenwei356/seqkit/releases/tag/v2.5.0)
- new command `seqkit merge-slides`: merge sliding windows generated from seqkit sliding. [#390](https://github.com/shenwei356/seqkit/issues/390)
- `seqkit stats`:
- added a new flag `-N/--N` for appending other N50-like stats as new columns. [#393](https://github.com/shenwei356/seqkit/issues/393)
- added a progress bar for > 1 input files.
- write the result of each file immediately (no output buffer) when using `-T/--tabular`.
- `seqkit translate`:
- add options `-s/--out-subseqs` and `-m/--min-len` to write ORFs longer than `x` amino acids as individual records. [#389](https://github.com/shenwei356/seqkit/issues/389)
- `seqkit sum`:
- do not remove possible '*' by default and delete confusing warnings. Thanks to @photocyte. [#399](https://github.com/shenwei356/seqkit/issues/399)
- added a progress bar for > 1 input files.
- `seqkit pair`:
- remove the restriction of requiring FASTQ format, i.e., FASTA files are also supported.
- `seqkit seq`:
- update help messages. [#387](https://github.com/shenwei356/seqkit/issues/387)
- `seqkit fxtab`:
- faster alphabet computation (`-a/--alphabet`) with a new data structure. Thanks to @elliotwutingfeng [#388](https://github.com/shenwei356/seqkit/pull/388)
- `seqkit subseq`:
- accept reverse coordinates in BED/GTF. [#392](https://github.com/shenwei356/seqkit/issues/392)
- [SeqKit v2.4.0](https://github.com/shenwei356/seqkit/releases/tag/v2.4.0) - 2023-03-17
[](https://github.com/shenwei356/seqkit/releases/tag/v2.4.0)
- `seqkit`:
- **support `bzip2` format**. [#361](https://github.com/shenwei356/seqkit/issues/361)
- support setting compression level for `gzip`, `zstd`, and `bzip2` format via `--compress-level`. [#320](https://github.com/shenwei356/seqkit/issues/320)
- the global flag `--infile-list` accepts stdin (`-`) now.
- wrap the help message of flags.
- `seqkit locate`:
- **do not remove embeded regions when searching with regular expressions**. [#368](https://github.com/shenwei356/seqkit/issues/368)
- `seqkit amplicon`:
- fix BED coordinates for amplicons found in the minus strand. [#367](https://github.com/shenwei356/seqkit/issues/367)
- `seqkit split`:
- fix forgetting to add extension for `--two-pass`. [#332](https://github.com/shenwei356/seqkit/issues/332)
- `seqkit stats`:
- fix compute Q1 and Q3 of sequence length for one record. [#353](https://github.com/shenwei356/seqkit/issues/353)
- `seqkit grep`:
- fix count number (`-C`) for matching with mismatch (`-m > 0`). [#370](https://github.com/shenwei356/seqkit/issues/370)
- `seqkit replace`:
- **add some flags to match partly records to edit**; these flags are transplanted from `seqkit grep`. [#348](https://github.com/shenwei356/seqkit/issues/348)
- `seqkit faidx`:
- **allow empty lines at the end of sequences**.
- `seqkit faidx/sort/shuffle/split/subseq`:
- **new flag `-U/--update-faidx`: update the FASTA index file if it exists, to guarantee the index file matches the FASTA files**. [#364](https://github.com/shenwei356/seqkit/issues/364)
- improve log info and update help message. [#365](https://github.com/shenwei356/seqkit/issues/365)
- `seqkit seq`:
- allow filtering sequences of length zero. thanks to @penglbio.
- `seqkit rename`:
- new flag `-s/--separator` for setting separator between original ID/name and the counter (default "_"). [#360](https://github.com/shenwei356/seqkit/issues/360)
- new flag `-N/--start-num` for setting starting count number for duplicated IDs/names (default 2). [#360](https://github.com/shenwei356/seqkit/issues/360)
- new flag `-1/--rename-1st-rec` for renaming the first record as well. [#360](https://github.com/shenwei356/seqkit/issues/360)
- do not append space if there's no description after the sequene ID.
- `seqkit sliding`:
- new flag `-S/--suffix` for change the suffix added to the sequence ID (default: "_sliding").
- [SeqKit v2.3.1](https://github.com/shenwei356/seqkit/releases/tag/v2.3.1) - 2022-09-22
[](https://github.com/shenwei356/seqkit/releases/tag/v2.3.1)
- `seqkit grep/locate`: fix bug of FMIndex building for empty sequences. [#321](https://github.com/shenwei356/seqkit/issues/321)
- `seqkit split2`: fix bug of splitting two FASTA files. [#325](https://github.com/shenwei356/seqkit/issues/325)
- `seqkit faidx`: `--id-regexp` works now.
- [SeqKit v2.3.0](https://github.com/shenwei356/seqkit/releases/tag/v2.3.0) - 2022-08-12
[](https://github.com/shenwei356/seqkit/releases/tag/v2.3.0)
- `seqkit grep/rename`:
- *reduce memory comsumption for a lot of searching patterns, and it's faster*. [#305](https://github.com/shenwei356/seqkit/issues/305)
- 2X faster `-s/--by-seq`.
- `seqkit split`
- fix outputting an empty file when the number of sequence equal to the split size. [#293](https://github.com/shenwei356/seqkit/issues/293)
- add options to set output file prefix and extention. [#296](https://github.com/shenwei356/seqkit/issues/296)
- `seqkit split2`
- reduce memory consumption. [#304](https://github.com/shenwei356/seqkit/issues/304)
- add options to set output file prefix
- `seqkit stats`:
- add GC content. [#294](https://github.com/shenwei356/seqkit/issues/294)
- [SeqKit v2.2.0](https://github.com/shenwei356/seqkit/releases/tag/v2.2.0) - 2020-03-14
[](https://github.com/shenwei356/seqkit/releases/tag/v2.2.0)
- `seqkit`:
- **add support of `xz` and `zstd` input/output formats**. [#274](https://github.com/shenwei356/seqkit/issues/274)
- fix panic when reading records with header of `ID` + blanks.
- **new command `seqkit sum`: computing message digest for all sequences in FASTA/Q files**.
The idea comes from @photocyte and the format borrows from [seqhash](https://github.com/TimothyStiles/poly/tree/prime/seqhash) [#262](https://github.com/shenwei356/seqkit/issues/262)
- new command `seqkit fa2fq`: retrieving corresponding FASTQ records by a FASTA file
- `seqkit split2`:
- new flag `-e/--extension` for forcing compresson or changing compression format. [#276](https://github.com/shenwei356/seqkit/issues/276)
- support changing output prefix via `-o/--out-file`. [#275](https://github.com/shenwei356/seqkit/issues/275)
- `seqkit concat`:
- fix handling of multiple seqs with the same ID in one file. [#269](https://github.com/shenwei356/seqkit/issues/269)
- performaning out/full join. [#270](https://github.com/shenwei356/seqkit/issues/270)
- preserve the comments. [#271](https://github.com/shenwei356/seqkit/issues/271)
- `seqkit locate`:
- parallelizing `-F/--use-fmi` and `-m` for large number of search patterns.
- `seqkit amplicon`:
- new flag `-M/--output-mismatches` to append the total mismatches and mismatches of 5' end and 3' end. [#286](https://github.com/shenwei356/seqkit/issues/286)
- `seqkit grep`:
- detect FASTA/Q symbol `@` and `>` in the searching patterns and show warnings.
- add new flag `-C/--count`, like `grep -c` in GNU grep. [#267](https://github.com/shenwei356/seqkit/issues/267)
- `seqkit range`:
- support removing leading 100 seqs (`seqkit range -r 101:-1` == `tail -n +101`). [#279](https://github.com/shenwei356/seqkit/issues/279)
- `seqkit subseq`:
- report error when no options were given.
- update doc:
- `seqkit head`: add doc for "seqkit tail": `seqkit range -N:-1 seqs.fasta`. [#272](https://github.com/shenwei356/seqkit/issues/272)
- `seqkit rmdup`: add the note of only the first record being saved for duplicates. [#265](https://github.com/shenwei356/seqkit/issues/265)
- [SeqKit v2.1.0](https://github.com/shenwei356/seqkit/releases/tag/v2.1.0) - 2021-11-15
[](https://github.com/shenwei356/seqkit/releases/tag/v2.1.0)
- `seqkit seq`:
- **fix filtering by average quality `-Q/-R`**. [#257](https://github.com/shenwei356/seqkit/issues/257)
- `seqkit convert`:
- fix quality encoding checking, change default value of `-N/--thresh-B-in-n-most-common` from `4` to `2`.
[#254](https://github.com/shenwei356/seqkit/issues/254) and [#239](https://github.com/shenwei356/seqkit/issues/239])
- `seqkit split`:
- fix writing an extra empty file when using `--two-pass`[#244](https://github.com/shenwei356/seqkit/issues/244)
- `seqkit subseq`:
- fix `--bed` which fail to recognize strand `.`.
- `seqkit fq2fa`:
- faster, and do not wrap sequences.
- `seqkit grep/locate/mutate`:
- detect unquoted comma and show warning message, e.g., `-p 'A{2,}'`. [#250](https://github.com/shenwei356/seqkit/issues/250)
- [SeqKit v2.0.0](https://github.com/shenwei356/seqkit/releases/tag/v2.0.0) - 2021-08-27
[](https://github.com/shenwei356/seqkit/releases/tag/v2.0.0)
- **Performance improvements**
- `seqkit`:
- **faster FASTA/Q reading and writing, especially on FASTQ**, see the [benchmark](https://github.com/shenwei356/bio/tree/1e130b6b973e5321bc0e508316716f763cd6f304#fastaq-reading-and-writing).
- reading (plain text): 4X faster. `seqkit stats dataset_C.fq`
- reading (gzip files): 45% faster. `seqkit stats dataset_C.fq.gz`
- reading + writing (plain text): 3.5X faster. `seqkit grep -p . -v dataset_C.fq -o t`
- reading + writing (gzip files): 2.2X faster. `seqkit grep -p . -v dataset_C.fq.gz -o t.gz`
- **change default value of `-j/--threads` from 2 to 4**, which is faster for writting gzip files.
- `seqkit seq`:
- **fix writing speed, which was slowed down in v0.12.1**.
- **Breaking changes**
- `seqkit grep/rmdup/common`:
- **consider reverse complement sequence by default for comparing by sequence**, add flag `-P/--only-positive-strand`. [#215](https://github.com/shenwei356/seqkit/issues/215)
- `seqkit rename`:
- **rename ID only, do not append original header to new ID**. [#236](https://github.com/shenwei356/seqkit/issues/236)
- `seqkit fx2tab`:
- for `-s/--seq-hash`: outputing MD5 instead of hash value (integers) of xxhash. [#219](https://github.com/shenwei356/seqkit/issues/219)
- **Bugfixes**
- `seqkit seq`:
- **fix failing to output gzipped format for file name with extension of `.gz` since v0.12.1**.
- `seqkit tab2fx`:
- fix bug for very long sequences. [#214](https://github.com/shenwei356/seqkit/issues/214)
- `seqkit fish`:
- fix range check. [#213](https://github.com/shenwei356/seqkit/issues/213)
- `seqkit grep`:
- it's not exactly a bug: forgot to use multi-threads for `-m` > 0.
- **New features/enhancements**
- `seqkit grep`:
- allow empty pattern files.
- `seqkit faidx`:
- support region with `begin > end`, i.e., **returning reverse complement sequence**
- add new flag `-l/--region-file`: file containing a list of regions.
- `seqkit fx2tab`:
- new flag `-Q/--no-qual` for disabling outputing quality even for FASTQ file. [#221](https://github.com/shenwei356/seqkit/issues/221)
- `seqkit amplicon`:
- new flag `-u/--save-unmatched` for saving records that do not match any primer.
- `seqkit sort`:
- new flag `-b/--by-bases` for sorting by non-gap bases, for multiple sequence alignment files.[#216](https://github.com/shenwei356/seqkit/issues/216)
- [SeqKit v0.16.1](https://github.com/shenwei356/seqkit/releases/tag/v0.16.1) - 2021-05-20
[](https://github.com/shenwei356/seqkit/releases/tag/v0.16.1)
- `seqkit shuffle --two-pass`: fix bug introduced in [#173](https://github.com/shenwei356/seqkit/issues/173) . [#209](https://github.com/shenwei356/seqkit/issues/209)
- `seqkit pair`: fix a dangerous bug: when input files are not in current directory, input files were overwritten.
- [SeqKit v0.16.0](https://github.com/shenwei356/seqkit/releases/tag/v0.16.0) - 2021-04-16
[](https://github.com/shenwei356/seqkit/releases/tag/v0.16.0)
- new command `seqkit head-genome`:
- print sequences of the first genome with common prefixes in name
- `seqkit grep/locate/amplicon -m`
- *much faster (300-400x) searching with mismatch allowed* by optimizing FM-indexing and parallelization.
- new flag `-I/--immediate-output`.
- `seqkit grep/locate`:
- fix bug of `-m` when querying contains letters not in alphabet, usually for protein sequences. [#178](https://github.com/shenwei356/seqkit/issues/178), [#179](https://github.com/shenwei356/seqkit/issues/179)
- onply search on positive strand when searching unlimited or protein sequences.
- `seqkit locate`:
- removing debug info for `-r` introduced in a0f6b6e. [#180](https://github.com/shenwei356/seqkit/issues/180)
- `seqkit amplicon`:
- fix bug of `-m`, when mismatch is allowed.
- `seqkit fx2tab`:
- new flag `-C/--base-count` for counting bases. [#183](https://github.com/shenwei356/seqkit/issues/183)
- `seqkit tab2fx`:
- fix a rare bug. [#197](https://github.com/shenwei356/seqkit/issues/197)
- `seqkit subseq`:
- fix bug for BED with empty columns. [#195](https://github.com/shenwei356/seqkit/issues/195)
- `seqkit genautocomplete`:
- **support bash|zsh|fish|powershell**.
- [SeqKit v0.15.0](https://github.com/shenwei356/seqkit/releases/tag/v0.15.0) - 2021-01-12
[](https://github.com/shenwei356/seqkit/releases/tag/v0.15.0)
- `seqkit grep/locate`: update help message.
- `seqkit grep`: **search on both strand when searching by sequence**.
- `seqkit split2`: fix redundant log when using `-s`.
- `seqkit bam`: new field `RightSoftClipSeq`. [#172](https://github.com/shenwei356/seqkit/pull/172)
- `seqkit sample -2`: remove extra `\n`. [#173](https://github.com/shenwei356/seqkit/issues/173)
- `seqkit split2 -l`: fix bug for splitting by accumulative length, this bug occurs when the first record is longer than `-l`, no sequences are lost.
- [SeqKit v0.14.0](https://github.com/shenwei356/seqkit/releases/tag/v0.14.0) - 2020-10-30
[](https://github.com/shenwei356/seqkit/releases/tag/v0.14.0)
- new command `seqkit pair`: match up paired-end reads from two fastq files, faster than fastq-pair.
- `seqkit translate`: new flag `-F/--append-fram` for optional adding frame info to ID. [#159](https://github.com/shenwei356/seqkit/issues/159)
- `seqkit stats`: reduce memory usage when using `-a` for calculating N50. [#153](https://github.com/shenwei356/seqkit/issues/153)
- `seqkit mutate`: fix inserting sequence `-i/--insertion`,
this bug occurs when `insert site` is big in some cases, don't worry if no error reported.
- `seqkit replace`:
- new flag `-U/--keep-untouched`: do not change anything when no value found for the key (only for sequence name).
- do no support editing FASTQ sequence.
- `seqkit grep/locate`: new flag `--circular` for supporting circular genome. [#158](https://github.com/shenwei356/seqkit/issues/158)
- [SeqKit v0.13.2](https://github.com/shenwei356/seqkit/releases/tag/v0.13.2) - 2020-07-13
[](https://github.com/shenwei356/seqkit/releases/tag/v0.13.2)
- `seqkit sana`: fix bug causing hanging on empty files. [#149](https://github.com/shenwei356/seqkit/pull/149)
- [SeqKit v0.13.1](https://github.com/shenwei356/seqkit/releases/tag/v0.13.1) - 2020-07-09
[](https://github.com/shenwei356/seqkit/releases/tag/v0.13.1)
- `seqkit sana`: fix bug causing hanging on empty files. [#148](https://github.com/shenwei356/seqkit/pull/148)
- [SeqKit v0.13.0](https://github.com/shenwei356/seqkit/releases/tag/v0.13.0) - 2020-07-07
[](https://github.com/shenwei356/seqkit/releases/tag/v0.13.0)
- `seqkit`: fix a rare FASTA/Q parser bug. [#127](https://github.com/shenwei356/seqkit/issues/127)
- `seqkit seq`: output sequence or quality in single line when `-s/--seq` or `-q/--qual` is on. [#132](https://github.com/shenwei356/seqkit/issues/132)
- `seqkit translate`: delete debug info, [#133](https://github.com/shenwei356/seqkit/issues/133), and fix typo. [#134](https://github.com/shenwei356/seqkit/issues/134)
- `seqkit split2`: tiny performance improvement. [#137](https://github.com/shenwei356/seqkit/issues/137)
- `seqkit stats`: new flag `-i/--stdin-label` for replacing default "-" for stdin. [#139](https://github.com/shenwei356/seqkit/issues/139)
- `seqkit fx2tab`: new flag `-s/--seq-hash` for printing hash of sequence (case sensitive). [#144](https://github.com/shenwei356/seqkit/issues/144)
- `seqkit amplicon`:
- fix bug of missing searching reverse strand. [#140](https://github.com/shenwei356/seqkit/issues/140)
- supporting degenerate bases now. [#83](https://github.com/shenwei356/seqkit/issues/83)
- new flag `-p/--primer-file` for reading list of primer pairs. [#142](https://github.com/shenwei356/seqkit/issues/142)
- new flag `--bed` for outputing in BED6+1 format. [#141](https://github.com/shenwei356/seqkit/issues/141)
- New features and improvements by [@bsipos](https://github.com/bsipos). [#130](https://github.com/shenwei356/seqkit/pull/130), [#147](https://github.com/shenwei356/seqkit/pull/147)
- new command `seqkit scat`, for real-time robust concatenation of fastx files.
- Rewrote the parser behind the `sana` subcommand, now it supports robust parsing of fasta file as well.
- Added a "toolbox" feature to the `bam` subcommand (`-T`), which is a collection of filters acting on streams of BAM records configured through a YAML string (see the docs for more).
- Added the `SEQKIT_THREADS` environmental variable to override the default number of threads.
- [SeqKit v0.12.1](https://github.com/shenwei356/seqkit/releases/tag/v0.12.1) - 2020-04-21
[](https://github.com/shenwei356/seqkit/releases/tag/v0.12.1)
- `seqkit bam`: add colorised and pretty printed output, by [@bsipos](https://github.com/bsipos). [#110](https://github.com/shenwei356/seqkit/pull/110)
- `seqkit locate/grep`: fix bug of `-m`, when query contains letters not in subject sequences. [#124](https://github.com/shenwei356/seqkit/issues/124)
- `seqkit split2`: new flag `-l/--by-length` for splitting into chunks of N bases.
- `seqkit fx2tab`:
- new flag `-I/--case-sensitive` for calculating case sensitive base content. [#108](https://github.com/shenwei356/seqkit/issues/108)
- add missing column name for averge quality for `-H -q`. [#115](https://github.com/shenwei356/seqkit/issues/115)
- fix output of `-n/--only-name`, do not write empty columns of sequence and quality. [#104](https://github.com/shenwei356/seqkit/issues/104), [#115](https://github.com/shenwei356/seqkit/issues/115)
- `seqkit seq`: new flag `-k/--color`: colorize sequences.
- [SeqKit v0.12.0](https://github.com/shenwei356/seqkit/releases/tag/v0.12.0) - 2020-02-18
[](https://github.com/shenwei356/seqkit/releases/tag/v0.12.0)
- `seqkit`:
- fix checking input file existence.
- new global flag `--infile-list` for long list of input files, if given, they are appended to files from cli arguments.
- `seqkit faidx`: supporting "truncated" (no ending newline charactor) file.
- `seqkit seq`:
- **do not force switching on `-g` when using `-m/-M`**.
- show recommendation if flag `-t/--seq-type` is not DNA/RNA when computing complement sequence. [#103](https://github.com/shenwei356/seqkit/issues/103)
- `seqkit translate`: supporting multiple frames. [#96](https://github.com/shenwei356/seqkit/issues/96)
- `seqkit grep/locate`:
- add detection and warning for space existing in search pattern/sequence.
- **speed improvement (2X) for `-m/--max-mismatch`**. [shenwei356/bwt/issues/3](https://github.com/shenwei356/bwt/issues/3)
- `seqkit locate`:
- new flag `-M/--hide-matched` for hiding matched sequences. [#98](https://github.com/shenwei356/seqkit/issues/98)
- **new flag `-r/--use-regexp` for explicitly using regular expression, so improve speed of default `index` operation. And you have to switch this on if using regexp now**.
[#101](https://github.com/shenwei356/seqkit/issues/101)
- **new flag `-F/--use-fmi` for improving search speed for lots of sequence patterns**.
- `seqkit rename`: making IDs unique across multiple files, and can write into multiple files. [#100](https://github.com/shenwei356/seqkit/issues/100)
- `seqkit sample`: fix stdin checking for flag `-2`. [#102](https://github.com/shenwei356/seqkit/issues/102).
- `seqkit rename/split/split2`: fix detection of existed outdir.
- `split split`: fix bug of `seqkit split -i -2` and parallizing it.
- `seqkit version`: checking update is optional (`-u`).
- [SeqKit v0.11.0](https://github.com/shenwei356/seqkit/releases/tag/v0.11.0) - 2019-09-25
[](https://github.com/shenwei356/seqkit/releases/tag/v0.11.0)
- `seqkit`: fix hanging when reading from truncated gzip file.
- new commands:
- `seqkit amplicon`: retrieve amplicon (or specific region around it) via primer(s).
- [new commands by @bsipos](https://github.com/shenwei356/seqkit/pull/81):
- `seqkit watch`: monitoring and online histograms of sequence features.
- `seqkit sana`: sanitize broken single line fastq files.
- `seqkit fish`: look for short sequences in larger sequences using local alignment.
- `seqkit bam`: monitoring and online histograms of BAM record features.
- `seqkit grep/locate`: reduce memory occupation when using flag `-m/--max-mismatch`.
- `seqkit seq`: fix panic of computing complement sequence for long sequences containing illegal letters without flag `-v` on. [#84](https://github.com/shenwei356/seqkit/issues/84)
- [SeqKit v0.10.2](https://github.com/shenwei356/seqkit/releases/tag/v0.10.2) - 2019-07-30
[](https://github.com/shenwei356/seqkit/releases/tag/v0.10.2)
- `seqkit`: fix bug of parsing sequence ID delimited by tab (`\t`). [#78](https://github.com/shenwei356/seqkit/issues/78)
- `seqkit grep`: better logic of `--delete-matched`.
- `seqkit common/rmdup/split`: use xxhash to replace MD5 when comparing with sequence, discard flag `-m/--md5`.
- `seqkit stats`: new flag `-b/--basename` for outputting basename instead of full path.
- [SeqKit v0.10.1](https://github.com/shenwei356/seqkit/releases/tag/v0.10.1) - 2019-02-27
[](https://github.com/shenwei356/seqkit/releases/tag/v0.10.1)
- `seqkit fx2tab`: new option `-q/--avg-qual` for outputting average read quality. [#60](https://github.com/shenwei356/seqkit/issues/60)
- `seqkit grep/locate`: fix support of `X` when using `-d/--degenerate`. [#61](https://github.com/shenwei356/seqkit/issues/61)
- `seqkit translate`:
- new flag `-M/--init-codon-as-M` to translate initial codon at beginning to 'M'. [#62](https://github.com/shenwei356/seqkit/issues/62)
- translates `---` to `-` for aligned DNA/RNA, flag `-X` needed. [#63](https://github.com/shenwei356/seqkit/issues/63)
- supports codons containing ambiguous bases, e.g., `GGN->G`, `ATH->I`. [#64](https://github.com/shenwei356/seqkit/issues/64)
- new flag `-l/--list-transl-table` to show details of translate table N
- new flag `-l/--list-transl-table-with-amb-codons` to show details of translate table N (including ambigugous codons)
- `seqkit split/split2`, fix bug of ignoring `-O` when reading from stdin.
- [SeqKit v0.10.0](https://github.com/shenwei356/seqkit/releases/tag/v0.10.0) - 2018-12-24
[](https://github.com/shenwei356/seqkit/releases/tag/v0.10.0)
- `seqkit`: report error when input is directory.
- new command `seqkit mutate`: edit sequence (point mutation, insertion, deletion).
- [SeqKit v0.9.3](https://github.com/shenwei356/seqkit/releases/tag/v0.9.3) - 2018-12-02
[](https://github.com/shenwei356/seqkit/releases/tag/v0.9.3)
- `seqkit stats`: fix panic for empty file. [#57](https://github.com/shenwei356/seqkit/issues/57)
- `seqkit translate`: add flag `-x/--allow-unknown-codon` to translate unknown codon to `X`.
- [SeqKit v0.9.2](https://github.com/shenwei356/seqkit/releases/tag/v0.9.2) - 2018-11-16
[](https://github.com/shenwei356/seqkit/releases/tag/v0.9.2)
- `seqkit`: stricter checking for value of global flag `-t/--seq-type`.
- `seqkit sliding`: fix bug for flag `-g/--greedy`. [#54](https://github.com/shenwei356/seqkit/issues/54)
- `seqkit translate`: fix bug for frame < 0. [#55](https://github.com/shenwei356/seqkit/issues/55)
- `seqkit seq`: add TAB to default blank characters (flag `-G/--gap-letters`), and fix filter result when using flag `-g/--remove-gaps` along with `-m/--min-len` or `-M/--max-len`
- [SeqKit v0.9.1](https://github.com/shenwei356/seqkit/releases/tag/v0.9.1) - 2018-10-12
[](https://github.com/shenwei356/seqkit/releases/tag/v0.9.1)
- `seqkit faidx`: fix bug of retrieving subsequence with multiple regions on same sequence. [#48](https://github.com/shenwei356/seqkit/issues/48)
- `seqkit sort/shuffle/split`: fix bug when using `-2/--two-pass` to process `.gz` files. [#52](https://github.com/shenwei356/seqkit/issues/52)
- [SeqKit v0.9.0](https://github.com/shenwei356/seqkit/releases/tag/v0.9.0) - 2018-09-26
[](https://github.com/shenwei356/seqkit/releases/tag/v0.9.0)
- `seqkit`: better handle of empty file, no error message shown. [#36](https://github.com/shenwei356/seqkit/issues/36)
- new subcommand `seqkit split2`: split sequences into files by size/parts (FASTA, PE/SE FASTQ). [#35](https://github.com/shenwei356/seqkit/issues/35)
- new subcommand `seqkit translate`: translate DNA/RNA to protein sequence. [#28](https://github.com/shenwei356/seqkit/issues/28)
- `seqkit sort`: fix bug when using `-2 -i`, and add support for sorting in natural order. [#39](https://github.com/shenwei356/seqkit/issues/39)
- `seqkit grep` and `seqkit locate`: add experimental support of mismatch when searching subsequences. [#14](https://github.com/shenwei356/seqkit/issues/14)
- `seqkit stats`: add stats of Q20 and Q30 for FASTQ. [#45](https://github.com/shenwei356/seqkit/issues/45)
- [SeqKit v0.8.1](https://github.com/shenwei356/seqkit/releases/tag/v0.8.1) - 2018-06-29
[](https://github.com/shenwei356/seqkit/releases/tag/v0.8.1)
- `seqkit`: do not call `pigz` or `gzip` for decompressing gzipped file any more. But you can still utilize `pigz` or `gzip` by `pigz -d -c seqs.fq.gz | seqkit xxx`.
- `seqkit subseq`: fix bug of missing quality when using `--gtf` or `--bed`
- `seqkit stats`: parallelize counting files, it's much faster for lots of small files, especially for files on SSD
- [SeqKit v0.8.0](https://github.com/shenwei356/seqkit/releases/tag/v0.8.0) - 2018-03-22
[](https://github.com/shenwei356/seqkit/releases/tag/v0.8.0)
- `seqkit`, **stricter FASTA/Q format requirement**, i.e., must starting with `>` or `@`.
- `seqkit`, *fix output format for FASTQ files containing zero-length records*, yes this [happens](https://github.com/lh3/seqtk/issues/109).
- `seqkit`, add amino acid code `O` (pyrrolysine) and `U` (selenocysteine).
- `seqkit replace`, *add flag `--nr-width` to fill leading 0s for `{nr}`*, useful for preparing sequence submission (">strain_00001 XX", ">strain_00002 XX").
- `seqkit subseq`, require BED file to be tab-delimited.
- [SeqKit v0.7.2](https://github.com/shenwei356/seqkit/releases/tag/v0.7.2) - 2017-12-03
[](https://github.com/shenwei356/seqkit/releases/tag/v0.7.2)
- `seqkit tab2fx`: fix a concurrency bug that occurs in low proprobability
when only 1-column data provided.
- `seqkit stats`: add quartiles of sequence length
- `seqkit faidx`: add support for retrieving subsequence using seq ID and region,
which is similar with "samtools faidx" but has some extra features
- [SeqKit v0.7.1](https://github.com/shenwei356/seqkit/releases/tag/v0.7.1) - 2017-09-22
[](https://github.com/shenwei356/seqkit/releases/tag/v0.7.1)
- `seqkit convert`: fix bug of read quality containing only 3 or less values. [shenwei356/bio/issues/3](https://github.com/shenwei356/bio/issues/3)
- `seqkit stats`: add option `-T/--tabular` to output in machine-friendly tabular format. [#23](https://github.com/shenwei356/seqkit/issues/23)
- `seqkit common`: increase speed and decrease memory occupation, and add some notes.
- fix some typos. [#22](https://github.com/shenwei356/seqkit/issues/22)
- suggestion: please **install [pigz](http://zlib.net/pigz/) to gain better parsing performance for gzipped data**.
- [SeqKit v0.7.0](https://github.com/shenwei356/seqkit/releases/tag/v0.7.0) - 2017-08-12
[](https://github.com/shenwei356/seqkit/releases/tag/v0.7.0)
- add new command `convert` for converting FASTQ quality encoding between Sanger, Solexa and Illumina. Thanks suggestion from [@cviner](https://github.com/cviner) ( [#18](https://github.com/shenwei356/seqkit/issues/18)). [usage & example](http://bioinf.shenwei.me/seqkit/usage/#convert).
- add new command `range` for printing FASTA/Q records in a range (start:end). [#19](https://github.com/shenwei356/seqkit/issues/19). [usage & example](http://bioinf.shenwei.me/seqkit/usage/#range).
- add new command `concate` for concatenating sequences with same ID from multiple files. [usage & example](http://bioinf.shenwei.me/seqkit/usage/#concate).
- [SeqKit v0.6.0](https://github.com/shenwei356/seqkit/releases/tag/v0.6.0) - 2017-06-21
[](https://github.com/shenwei356/seqkit/releases/tag/v0.6.0)
- add new command `genautocomplete` to generate **shell autocompletion** script! ([#17](https://github.com/shenwei356/seqkit/issues/17))
- add new command `seqkit dup` for duplicating sequences ([#16](https://github.com/shenwei356/seqkit/issues/16))
- `seqkit stats -a` does not show L50 which may brings confusion ([#15](https://github.com/shenwei356/seqkit/issues/15))
- `seqkit subseq --bed`: more robust for bad BED files
- [SeqKit v0.5.5](https://github.com/shenwei356/seqkit/releases/tag/v0.5.5) - 2017-05-10
[](https://github.com/shenwei356/seqkit/releases/tag/v0.5.5)
- Increasing speed of reading `.gz` file by utilizing `gzip` (1.3X),
it would be much faster if you installed `pigz` (2X).
- ***Fixing colorful output in Windows***
- `seqkit locate`: ***add flag `--gtf` and `--bed` to output GTF/BED6 format,
so the result can be used in `seqkit subseq`***.
- `seqkit subseq`: fix bug of `--bed`, add checking coordinate.
- [SeqKit v0.5.4](https://github.com/shenwei356/seqkit/releases/tag/v0.5.4) - 2017-04-11
[](https://github.com/shenwei356/seqkit/releases/tag/v0.5.4)
- `seqkit subseq --gtf`, add flag `--gtf-tag` to set tag that's outputted as sequence comment
- fix `seqkit split` and `seqkit sample`: forget not to wrap sequence and quality in output for FASTQ format
- compile with go1.8.1
- [SeqKit v0.5.3](https://github.com/shenwei356/seqkit/releases/tag/v0.5.3) - 2017-04-01
[](https://github.com/shenwei356/seqkit/releases/tag/v0.5.3)
- `seqkit grep`: fix bug when using `seqkit grep -r -f patternfile`:
all records will be retrived due to failing to discarding the blank pattern (`""`). #11
- [SeqKit v0.5.2](https://github.com/shenwei356/seqkit/releases/tag/v0.5.2) - 2017-03-24
[](https://github.com/shenwei356/seqkit/releases/tag/v0.5.2)
- `seqkit stats -a` and `seqkit seq -g -G`: change default gap letters from '- ' to '- .'
- `seqkit subseq`: fix bug of range overflow when using `-d/--down-stream`
or `-u/--up-stream` for retieving subseq using BED (`--beb`) or GTF (`--gtf`) file.
- `seqkit locate`: add flag `-G/--non-greedy`, non-greedy mode,
faster but may miss motifs overlaping with others.
- [SeqKit v0.5.1](https://github.com/shenwei356/seqkit/releases/tag/v0.5.1) - 2017-03-12
[](https://github.com/shenwei356/seqkit/releases/tag/v0.5.1)
- `seqkit restart`: fix bug of flag parsing
- [SeqKit v0.5.0](https://github.com/shenwei356/seqkit/releases/tag/v0.5.0) - 2017-03-11
[](https://github.com/shenwei356/seqkit/releases/tag/v0.5.0)
- **new command `seqkit restart`, for resetting start position for circular genome**.
- `seqkit sliding`: add flag `-g/--greedy`, exporting last subsequences even shorter than windows size.
- `seqkit seq`:
- **add flag `-m/--min-len` and `-M/--max-len` to filter sequences by length**.
- rename flag `-G/--gap-letter` to `-G/--gap-letters`.
- `seqkit stat`:
- renamed to `seqkit stats`, don't worry, old name is still available as an alias.
- **add new flag `-a/all`, for all statistics, including `sum_gap`, `N50`, and `L50`**.
- [SeqKit v0.4.5](https://github.com/shenwei356/seqkit/releases/tag/v0.4.5) - 2017-02-26
[](https://github.com/shenwei356/seqkit/releases/tag/v0.4.5)
- `seqkit seq`: fix bug of failing to reverse quality of FASTQ sequence
- [SeqKit v0.4.4](https://github.com/shenwei356/seqkit/releases/tag/v0.4.4) - 2017-02-17
[](https://github.com/shenwei356/seqkit/releases/tag/v0.4.4)
- `seqkit locate`: fix bug of missing regular-expression motifs containing
non-DNA characters (e.g., `ACT.{6,7}CGG`) from motif file (`-f`).
- compiled with go v1.8.
- [SeqKit v0.4.3](https://github.com/shenwei356/seqkit/releases/tag/v0.4.3) - 2016-12-22
[](https://github.com/shenwei356/seqkit/releases/tag/v0.4.3)
- fix bug of `seqkit stat`: `min_len` always be `0` in versions: v0.4.0, v0.4.1, v0.4.2
- [SeqKit v0.4.2](https://github.com/shenwei356/seqkit/releases/tag/v0.4.2) - 2016-12-21
[](https://github.com/shenwei356/seqkit/releases/tag/v0.4.2)
- fix header information of `seqkit subseq` when restriving up- and down-steam
sequences using GTF/BED file.
- [SeqKit v0.4.1](https://github.com/shenwei356/seqkit/releases/tag/v0.4.1) - 2016-12-16
[](https://github.com/shenwei356/seqkit/releases/tag/v0.4.1)
- enchancement: remove redudant regions for `seqkit locate`.
- [SeqKit v0.4.0](https://github.com/shenwei356/seqkit/releases/tag/v0.4.0) - 2016-12-07
[](https://github.com/shenwei356/seqkit/releases/tag/v0.4.0)
- fix bug of `seqkit locate`, e.g, only find two locations
(`1-4`, `7-10`, missing `4-7`) of `ACGA` in `ACGACGACGA`.
- better output of `seqkit stat` for empty file.
- [SeqKit v0.3.9](https://github.com/shenwei356/seqkit/releases/tag/v0.3.9) - 2016-12-04
[](https://github.com/shenwei356/seqkit/releases/tag/v0.3.9)
- fix bug of region selection for blank sequences. affected commands include
`seqkit subseq --region`, `seqkit grep --region`, `seqkit split --by-region`.
- compile with go1.8beta1.
- [SeqKit v0.3.8.1](https://github.com/shenwei356/seqkit/releases/tag/v0.3.8.1) - 2016-11-25
[](https://github.com/shenwei356/seqkit/releases/tag/v0.3.8.1)
- enhancement and bugfix of `seqkit common`: two or more same files allowed,
fix log information of number of extracted sequences in the first file.
- [SeqKit v0.3.8](https://github.com/shenwei356/seqkit/releases/tag/v0.3.8) - 2016-12-24
[](https://github.com/shenwei356/seqkit/releases/tag/v0.3.8)
- enhancement of `seqkit common`: better handling of files containing replicated sequences
- [SeqKit v0.3.7](https://github.com/shenwei356/seqkit/releases/tag/v0.3.7) - 2016-12-23
[](https://github.com/shenwei356/seqkit/releases/tag/v0.3.7)
- fix bug in `seqkit split --by-id` when sequence ID contains invalid characters for system path.
- add more flags validation for `seqkit replace`.
- enhancement: raise error when key pattern matches multiple targes in cases of replacing with key-value files and more controls are added.
- changes: do not wrap sequence and quality in output for FASTQ format.
- [SeqKit v0.3.6](https://github.com/shenwei356/seqkit/releases/tag/v0.3.6) - 2016-11-03
[](https://github.com/shenwei356/seqkit/releases/tag/v0.3.6)
- add new feature for `seqkit grep`: new flag `-R` (`--region`) for specifying sequence region for searching.
- [SeqKit v0.3.5](https://github.com/shenwei356/seqkit/releases/tag/v0.3.5) - 2016-10-30
[](https://github.com/shenwei356/seqkit/releases/tag/v0.3.5)
- fig bug of `seqkit grep`: flag `-i` (`--ignore-case`) did not work when not using regular expression
- [SeqKit v0.3.4.1](https://github.com/shenwei356/seqkit/releases/tag/v0.3.4.1) - 2016-09-21
[](https://github.com/shenwei356/seqkit/releases/tag/v0.3.4.1)
- improve performance of reading (~10%) and writing (100%) gzip-compressed file
by using `github.com/klauspost/pgzip` package
- add citation
- [SeqKit v0.3.4](https://github.com/shenwei356/seqkit/releases/tag/v0.3.4) - 2016-09-17
[](https://github.com/shenwei356/seqkit/releases/tag/v0.3.4)
- bugfix: `seq` wrongly handles only the first one sequence file when multiple files given
- new feature: `fx2tab` can output alphabet letters of a sequence by flag `-a` (`--alphabet`)
- new feature: new flag `-K` (`--keep-key`) for `replace`, when replacing
with key-value file, one can choose keeping the key as value or not.
- [SeqKit v0.3.3](https://github.com/shenwei356/seqkit/releases/tag/v0.3.3) - 2016-08-18
[](https://github.com/shenwei356/seqkit/releases/tag/v0.3.3)
- fix bug of `seqkit replace`, wrongly starting from 2 when using `{nr}`
in `-r` (`--replacement`)
- new feature: `seqkit replace` supports replacement symbols `{nr}` (record number)
and `{kv}` (corresponding value of the key ($1) by key-value file)
- [SeqKit v0.3.2](https://github.com/shenwei356/seqkit/releases/tag/v0.3.2) - 2016-08-13
[](https://github.com/shenwei356/seqkit/releases/tag/v0.3.2)
- fix bug of `seqkit split`, error when target file is in a directory.
- improve performance of `seqkit spliding` for big sequences, and output
last part even if it's shorter than window sze,
output of FASTQ is also supported.
- [SeqKit v0.3.1.1](https://github.com/shenwei356/seqkit/releases/tag/v0.3.1.1) - 2016-08-07
[](https://github.com/shenwei356/seqkit/releases/tag/v0.3.1.1)
- compile with go1.7rc5, with ***higher performance and smaller size of binary file***
- [SeqKit v0.3.1](https://github.com/shenwei356/seqkit/releases/tag/v0.3.1) - 2016-08-02
[](https://github.com/shenwei356/seqkit/releases/tag/v0.3.1)
- improve speed of `seqkit locate`
- [SeqKit v0.3.0](https://github.com/shenwei356/seqkit/releases/tag/v0.3.0) - 2016-07-28
[](https://github.com/shenwei356/seqkit/releases/tag/v0.3.0)
- use fork of github.com/brentp/xopen, using `zcat` for speedup of .gz file
reading on \*nix systems.
- improve speed of parsing sequence ID when creating FASTA index
- reduce memory usage of `seqkit subseq --gtf`
- fix bug of `seqkit subseq` when using flag `--id-ncbi`
- fix bug of `seqkit split`, outdir error
- fix bug of `seqkit seq -p`, last base is wrongly failed to convert when
sequence length is odd.
- add "sum_len" result for output of `seqkit stat`
- [seqkit v0.2.9](https://github.com/shenwei356/seqkit/releases/tag/v0.2.9) - 2016-07-24
[](https://github.com/shenwei356/seqkit/releases/tag/v0.2.9)
- fix minor bug of `seqkit split` and `seqkit shuffle`,
header name error due to improper use of pointer
- add option `-O (--out-dir)` to `seqkit split`
- [seqkit v0.2.8](https://github.com/shenwei356/seqkit/releases/tag/v0.2.8) - 2016-07-19
[](https://github.com/shenwei356/seqkit/releases/tag/v0.2.8)
- improve speed of parsing sequence ID, not using regular expression for default `--id-regexp`
- improve speed of record outputing for small-size sequences
- fix minor bug: `seqkit seq` for blank record
- update benchmark result
- [seqkit v0.2.7](https://github.com/shenwei356/seqkit/releases/tag/v0.2.7) - 2016-07-18
[](https://github.com/shenwei356/seqkit/releases/tag/v0.2.7)
- ***reduce memory usage*** by optimize the outputing of sequences.
detail: using [`BufferedByteSliceWrapper`](https://godoc.org/github.com/shenwei356/util/byteutil#BufferedByteSliceWrapper) to resuse bytes.Buffer.
- ***reduce memory usage and improve speed*** by using custom buffered
reading mechanism, instead of using standard library `bufio`,
which is slow for large genome sequence.
- discard strategy of "buffer" and "chunk" of FASTA/Q records,
just parse records one by one.
- delete global flags `-c (--chunk-size)` and `-b (--buffer-size)`.
- add function testing scripts
- [seqkit v0.2.6](https://github.com/shenwei356/seqkit/releases/tag/v0.2.6) - 2016-07-01
[](https://github.com/shenwei356/seqkit/releases/tag/v0.2.6)
- fix bug of `seqkit subseq`: Inplace subseq method leaded to wrong result
- [seqkit v0.2.5.1](https://github.com/shenwei356/seqkit/releases/tag/v0.2.5.1)
[](https://github.com/shenwei356/seqkit/releases/tag/v0.2.5.1)
- fix a bug of `seqkit subseq`: chromesome name was not be converting to lower case when using `--gtf` or `--bed`
- [seqkit v0.2.5](https://github.com/shenwei356/seqkit/releases/tag/v0.2.5) - 2016-07-01
[](https://github.com/shenwei356/seqkit/releases/tag/v0.2.5)
- fix a serious bug brought in `v0.2.3`, using unsafe method to convert `string` to `[]byte`
- add awk-like built-in variable of record number (`{NR}`) for `seqkit replace`
- [seqkit v0.2.4.1](https://github.com/shenwei356/seqkit/releases/tag/v0.2.4.1) - 2016-06-12
[](https://github.com/shenwei356/seqkit/releases/tag/v0.2.4.1)
- fix several bugs from library `bio`, affected situations:
- Locating patterns in sequences by pattern FASTA file: `seqkit locate -f`
- Reading FASTQ file with record of which the quality starts with `+`
- add command `version`
- [seqkit v0.2.4](https://github.com/shenwei356/seqkit/releases/tag/v0.2.4) - 2016-05-31
[](https://github.com/shenwei356/seqkit/releases/tag/v0.2.4)
- add subcommand `head`
- [seqkit v0.2.3](https://github.com/shenwei356/seqkit/releases/tag/v0.2.3) - 2016-05-08
[](https://github.com/shenwei356/seqkit/releases/tag/v0.2.3)
- reduce memory occupation by avoid copy data when convert `string` to `[]byte`
- speedup reverse-complement by avoid repeatly calling functions
- [seqkit v0.2.2](https://github.com/shenwei356/seqkit/releases/tag/v0.2.2) - 2016-05-06
[](https://github.com/shenwei356/seqkit/releases/tag/v0.2.2)
- reduce memory occupation of subcommands that use FASTA index
- [seqkit v0.2.1](https://github.com/shenwei356/seqkit/releases/tag/v0.2.1) - 2016-05-02
[](https://github.com/shenwei356/seqkit/releases/tag/v0.2.1)
- improve performance of outputing.
- fix bug of `seqkit seq -g` for FASTA fromat
- some other minor fix of code and docs
- update benchmark results
- [seqkit v0.2.0](https://github.com/shenwei356/seqkit/releases/tag/v0.2.0) - 2016-04-29
[](https://github.com/shenwei356/seqkit/releases/tag/v0.2.0)
- ***reduce memory usage of writing output***
- fix bug of `subseq`, `shuffle`, `sort` when reading from stdin
- reduce memory usage of `faidx`
- make validating sequences an optional option in `seq` command, it saves some time.
- [seqkit v0.1.9](https://github.com/shenwei356/seqkit/releases/tag/v0.1.9) - 2016-04-26
[](https://github.com/shenwei356/seqkit/releases/tag/v0.1.9)
- using custom FASTA index file extension: `.seqkit.fai`
- reducing memory usage of `sample --number --two-pass`
- ***change default CPU number to 2 for multi-cpus computer, and 1 for single-CPU computer***
- [seqkit v0.1.8](https://github.com/shenwei356/seqkit/releases/tag/v0.1.8) - 2016-04-24
[](https://github.com/shenwei356/seqkit/releases/tag/v0.1.8)
- add subcommand `rename` to rename duplicated IDs
- add subcommand `faidx` to create FASTA index file
- ***utilize faidx to improve performance of `subseq`***
- *`shuffle`, `sort` and split support two-pass mode (by flag `-2`) with faidx to reduce memory usage.*
- document update
- [seqkit v0.1.7](https://github.com/shenwei356/seqkit/releases/tag/v0.1.7) - 2016-04-21
[](https://github.com/shenwei356/seqkit/releases/tag/v0.1.7)
- ***add support for (multi-line) FASTQ format***
- update document, add technical details
- rename subcommands `fa2tab` and `tab2fa` to `fx2tab` and `tab2fx`
- add subcommand `fq2fa`
- add column "seq_format" to `stat`
- add global flag `-b` (`--bufer-size`)
- little change of flag in `subseq` and some other commands
- [seqkit v0.1.6](https://github.com/shenwei356/seqkit/releases/tag/v0.1.6) - 2016-04-07
[](https://github.com/shenwei356/seqkit/releases/tag/v0.1.6)
- add subcommand `replace`
- [seqkit v0.1.5.2](https://github.com/shenwei356/seqkit/releases/tag/v0.1.5.2) - 2016-04-06
[](https://github.com/shenwei356/seqkit/releases/tag/v0.1.5.2)
- fix bug of `grep`, when not using flag `-r`, flag `-i` will not take effect.
- [seqkit v0.1.5.1](https://github.com/shenwei356/seqkit/releases/tag/v0.1.5.1)
[](https://github.com/shenwei356/seqkit/releases/tag/v0.1.5.1)
- fix result of `seqkit sample -n`
- fix benchmark script
- [seqkit v0.1.5](https://github.com/shenwei356/seqkit/releases/tag/v0.1.5) - 2016-03-29
[](https://github.com/shenwei356/seqkit/releases/tag/v0.1.5)
- add global flag `--id-ncbi`
- add flag `-d` (`--dup-seqs-file`) and `-D` (`--dup-num-file`) for subcommand `rmdup`
- make using MD5 as an optional flag `-m` (`--md5`) in subcommand `rmdup` and `common`
- fix file name suffix of `seqkit split` result
- minor modification of `sliding` output
- [seqkit v0.1.4.1](https://github.com/shenwei356/seqkit/releases/tag/v0.1.4.1) - 2016-03-27
[](https://github.com/shenwei356/seqkit/releases/tag/v0.1.4.1)
- change alignment of `stat` output
- preciser CPUs number control
- [seqkit v0.1.4](https://github.com/shenwei356/seqkit/releases/tag/v0.1.4) - 2016-03-25
[](https://github.com/shenwei356/seqkit/releases/tag/v0.1.4)
- add subcommand `sort`
- improve subcommand `subseq`: supporting of getting subsequences by GTF and BED files
- change name format of `sliding` result
- prettier output of `stat`
- [seqkit v0.1.3.1](https://github.com/shenwei356/seqkit/releases/tag/v0.1.3.1) - 2016-03-16
[](https://github.com/shenwei356/seqkit/releases/tag/v0.1.3.1)
- Performance improvement by reducing time of cleaning spaces
- Document update
- [seqkit v0.1.3](https://github.com/shenwei356/seqkit/releases/tag/v0.1.3) - 2016-03-15
[](https://github.com/shenwei356/seqkit/releases/tag/v0.1.3)
- **Further performance improvement**
- Rename sub command `extract` to `grep`
- Change default value of flag `--threads` back CPU number of current device,
change default value of flag `--chunk-size` back 10000 sequences.
- Update benchmark
- [seqkit v0.1.2](https://github.com/shenwei356/seqkit/releases/tag/v0.1.2) - 2016-03-14
[](https://github.com/shenwei356/seqkit/releases/tag/v0.1.2)
- Add flag `--dna2rna` and `--rna2dna` to subcommand `seq`.
- [seqkit v0.1.1](https://github.com/shenwei356/seqkit/releases/tag/v0.1.1) - 2016-03-13
[](https://github.com/shenwei356/seqkit/releases/download/v0.1.1)
- **5.5X speedup of FASTA file parsing** by avoid using regular expression to remove spaces ([detail](https://github.com/shenwei356/bio/commit/2457b877cf1b8d79d05adb1a8952f2dff9046eaf) ) and using slice indexing instead of map to validate letters ([detail](https://github.com/shenwei356/bio/commit/0f5912f6a3c6d737faacf9212f62d11c94e5044a))
- Change default value of global flag `-- thread` to 1. Since most of the subcommands are I/O intensive, For computation intensive jobs, like extract and locate, you may set a bigger value.
- Change default value of global flag `--chunk-size` to 100.
- Add subcommand `stat`
- Fix bug of failing to automatically detect alphabet when only one record in file.
- [seqkit v0.1](https://github.com/shenwei356/seqkit/releases/tag/v0.1) - 2016-03-11
[](https://github.com/shenwei356/seqkit/releases/tag/v0.1)
- first release of seqkit
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