extractfq

Extract some fastq reads (PE/SE) from the beginning of the files


Licenses
GPL-3.0/GPL-3.0+
Install
pip install extractfq==0.0.5

Documentation

extractfq

1 Introduction

extractfq is a tool to extract some fastq reads from the beginning of the files.

2 Installation

pip install extractfq

There will be a command extractfq created under the same directory as your pip command.

3 Usage

$ 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. [3]
  -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. [1500000]

Author

Guanliang MENG

Citation

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