Extract some fastq reads (PE/SE) from the beginning of the files
extractfq is a tool to extract some fastq reads from the beginning of the files.
pip install extractfq
There will be a command
extractfq created under the same directory as your
$ extractfq usage: extractfq.py [-h] [-fq1 <str>] [-fq2 <str>] [-outfq1 <str>] [-outfq2 <str>] [-size_required <float>] [-rl <int>] [-gz] [-cache_num <int>] Extract some fastq reads from the beginning of the files. Author: Guanliang Meng, see https://github.com/linzhi2013/extractfq. This script is part of the package `MitoZ`, when you use the script in your work, please cite: MitoZ: A toolkit for mitochondrial genome assembly, annotation and visualization with NGS data. Guangliang Meng, Yiyuan Li, Chentao Yang, Shanlin Liu (in manuscript) optional arguments: -h, --help show this help message and exit -fq1 <str> input fastq 1 file -fq2 <str> input fastq 2 file -outfq1 <str> output fastq 1 file -outfq2 <str> output fastq 2 file -size_required <float> size required in Gigabase.  -rl <int> read length required. discard the smaller ones, and cut the longer ones to this length [None] -gz gzip output. [False] -cache_num <int> the cache number of reads before writing to the file, to speed up. the larger of cache_num, the more memory (default is ca. 2G) will be used. 
This script is part of the package
MitoZ, when you use the script in your work, please cite:
Guanliang Meng, Yiyuan Li, Chentao Yang, Shanlin Liu. MitoZ: A toolkit for mitochondrial genome assembly, annotation and visualization; doi: https://doi.org/10.1101/489955
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