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Source: python-sqt
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders: Steffen Moeller <moeller@debian.org>
Section: science
Testsuite: autopkgtest-pkg-pybuild
Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-sequence-python3,
python3-all-dev,
python3-setuptools,
cython3,
python3-cutadapt <!nocheck>,
python3-pysam <!nocheck>,
python3-pytest <!nocheck>,
python3-seaborn <!nocheck>,
python3-xopen <!nocheck>
Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/python-sqt
Vcs-Git: https://salsa.debian.org/med-team/python-sqt.git
Homepage: https://bitbucket.org/marcelm/sqt
Rules-Requires-Root: no
Package: python3-sqt
Architecture: any
Section: python
Depends: ${shlibs:Depends},
${python3:Depends},
${misc:Depends},
python3-seaborn,
python3-matplotlib,
python3-pysam,
python3-cutadapt
Recommends: fonts-noto-color-emoji
Description: SeQuencing Tools for biological DNA/RNA high-throughput data
sqt is a collection of command-line tools for working with
high-throughput sequencing data. Conceptionally not fixed to use any
particular language, many sqt subcommands are currently implemented
in Python. For them, a Python package is available with functions for
reading and writing FASTA/FASTQ files, computing alignments, quality
trimming, etc.
.
The following tools are offered:
* sqt-coverage -- Compute per-reference statistics such as coverage
and GC content
* sqt-fastqmod -- FASTQ modifications: shorten, subset, reverse
complement, quality trimming.
* sqt-fastastats -- Compute N50, min/max length, GC content etc. of
a FASTA file
* sqt-qualityguess -- Guess quality encoding of one or more FASTA files.
* sqt-globalalign -- Compute a global or semiglobal alignment of two strings.
* sqt-chars -- Count length of the first word given on the command line.
* sqt-sam-cscq -- Add the CS and CQ tags to a SAM file with colorspace reads.
* sqt-fastamutate -- Add substitutions and indels to sequences in a
FASTA file.
* sqt-fastaextract -- Efficiently extract one or more regions from an
indexed FASTA file.
* sqt-translate -- Replace characters in FASTA files (like the 'tr'
command).
* sqt-sam-fixn -- Replace all non-ACGT characters within reads in a
SAM file.
* sqt-sam-insertsize -- Mean and standard deviation of paired-end
insert sizes.
* sqt-sam-set-op -- Set operations (union, intersection, ...) on
SAM/BAM files.
* sqt-bam-eof -- Check for the End-Of-File marker in compressed
BAM files.
* sqt-checkfastqpe -- Check whether two FASTQ files contain correctly
paired paired-end data.
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