fastqs2fastq.py - merge reads in fastq files

Tags

Genomics NGS FASTQ FASTQ Manipulation

Purpose

This script takes two paired-ended fastq files and outputs a single fastq file in which reads have merged.

The two files must be sorted by read identifier.

Note that this script is currently a proof-of-principle implementation and has not been optimized for speed or functionality.

Usage

Example:

python fastqs2fastq.py myReads.1.fastq.gz myReads.2.fastq.gz
       --method=join
       > join.fastq

In this example we take a pair of fastq files, join the reads and save the output in join.fastq.

Type:

python fastqs2fastq.py --help

for command line help.

Command line options

usage: fastqs2fastq [-h] [-m {join}] [--timeit TIMEIT_FILE]
                    [--timeit-name TIMEIT_NAME] [--timeit-header]
                    [--random-seed RANDOM_SEED] [-v LOGLEVEL]
                    [--log-config-filename LOG_CONFIG_FILENAME]
                    [--tracing {function}] [-? ?] [-I STDIN] [-L STDLOG]
                    [-E STDERR] [-S STDOUT]
fastqs2fastq: error: argument -?: expected one argument