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Extract some fastq reads from the beginning of the files

Project description

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]

Extract some fastq reads from the beginning of the files. Author:
mengguanliang@foxmail.com

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]

Author

Guanliang MENG

Citation

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)

Project details


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