README
¶
bio
A lightweight and high-performance (see seqkit benchmark) bioinformatics package.
FASTA/Q parsing
This package has high performance close to the famous C lib
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:
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
(Version 1.1-r92-dirty,
using kseq.h)
and seqkit
(Version 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 is used to assess running time
and peak memory usage.
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.
Copyright (c) 2013-2016, Wei Shen (shenwei356@gmail.com)
Directories
¶
| Path | Synopsis |
|---|---|
|
featio
|
|
|
_bed
Package bed is used to read bed features.
|
Package bed is used to read bed features. |
|
gtf
Package gtf is used to read gtf features.
|
Package gtf is used to read gtf features. |
|
Package seq balabala This package defines a *Seq* type, and provides some basic operations of sequence, like validation of DNA/RNA/Protein sequence and getting reverse complement sequence.
|
Package seq balabala This package defines a *Seq* type, and provides some basic operations of sequence, like validation of DNA/RNA/Protein sequence and getting reverse complement sequence. |
|
seqio
|
|
|
fai
Package fai implements fasta sequence file index handling, including creating , reading and random accessing.
|
Package fai implements fasta sequence file index handling, including creating , reading and random accessing. |
|
fastx
Package fastx seamlessly parses FASTA and FASTQ format file This package seamlessly parses both FASTA and FASTQ formats.
|
Package fastx seamlessly parses FASTA and FASTQ format file This package seamlessly parses both FASTA and FASTQ formats. |