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