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bio
===
[](https://godoc.org/github.com/shenwei356/bio)
[](https://goreportcard.com/report/github.com/shenwei356/bio)
A lightweight and high-performance
(see [seqkit](https://github.com/shenwei356/seqkit#benchmark) benchmark)
bioinformatics package.
FASTA/Q parsing
-----------------------
***This package has high performance close to the famous C lib
[`kseq.h`](https://github.com/attractivechaos/klib/blob/master/kseq.h).***
To test the performance, three datasets are used:
- dataset_A, bacteria genomes, 2.7G
- dataset_B, human genome, 2.9G
- dataset_C, Illumina reads, 2.2G
Summary by [`seqkit`](https://github.com/shenwei356/seqkit):
file seq_format seq_type num_seqs min_len avg_len max_len
dataset_A.fa FASTA DNA 67,748 56 41,442.5 5,976,145
dataset_B.fa FASTA DNA 194 970 15,978,096.5 248,956,422
dataset_C.fq FASTQ DNA 9,186,045 100 100 100
[`seqtk`](https://github.com/lh3/seqtk/)
(Version [1.1-r92-dirty](https://github.com/lh3/seqtk/tree/fb85aad4ce1fc7b3d4543623418a1ae88fe1cea6),
using `kseq.h`)
and [`seqkit`](https://github.com/shenwei356/seqkit)
(Version [v0.3.1.1](https://github.com/shenwei356/seqkit/releases/tag/v0.3.1.1),
using this package) were used to test.
**Note** that `seqtk` does not support wrapped (fixed line width) ouputing, so `seqkit` uses
`-w 0` to disable outputing wrapping.
Script [`memusg`](https://github.com/shenwei356/memusg) is used to assess running time
and peak memory usage.
[Commands](https://github.com/shenwei356/bio/blob/master/benchmark/run_benchmark_01_parse.sh)
Tests were repeated 5 times and average time and memory usage were computed.
Results:
Install
-------
This package is "go-gettable", just:
go get -u github.com/shenwei356/bio
More
----
See the README of sub package.
Documentation
-------------
[See documentation on godoc for more detail](https://godoc.org/github.com/shenwei356/bio/).
Copyright (c) 2013-2016, Wei Shen (shenwei356@gmail.com)
[MIT License](https://github.com/shenwei356/bio/blob/master/LICENSE)
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