pySeqkit

Toolkit for processing sequences in FASTA/Q formats

1. Introduction

pySeqkit is a toolkit for processing sequences in FASTA or FASTQ formats, it is writen in python and still under development. To install it, you can

git clone https://github.com/FlyPythons/pySeqkit.git

• This toolkit has been tested in python2.7

2. Example

pySeqkit has two sub commands(stat, split) now.

stat-Statistics on sequence files(fastA/Q)

• for FASTA/Q files, different formatted files can be stat together

python pySeqkit.py stat 1.fq *.fa > in.stat

• use '-c' to speed up the process

python pySeqkit.py stat -c 10 1.fq *.fa > in.stat

• for one file contains FASTA/Q file paths

python pySeqkit.py stat -f -c 10 in.fofn > in.stat

• for NGS short reads, you'd better turn on '-ngs' to avoid meaningless stat

python pySeqkit.py stat -ngs -c 10 *.R1.fq *.R2.fq

split-Split sequence files(fastA/Q)

• split by sequences number == {max number} per file

python pySeqkit.py split -m number -n {max number} -o split in.fa
python pySeqkit.py split -m number -n {max number} -o split in.fq

• split by sequences length ~= {max length} per file

python pySeqkit.py split -m length -n {max length} -o split in.fa
python pySeqkit.py split -m length -n {max length} -o split in.fq