extract_reads_from_interleaved_file.py – Extract reads from an interleaved file.¶
Description:
This script takes an interleaved file, like the ones produced by JGI, and outputs a forward and reverse fastq file with the corresponding reads in each file.
Usage: extract_reads_from_interleaved_file.py [options]
Input Arguments:
Note
[REQUIRED]
- -i, --input_fp
- Path to input forward reads in FASTQ format.
- -o, --output_dir
- Directory to store result files
[OPTIONAL]
- --forward_read_identifier
- This is the string identifying the forward reads. [default: 1:N:0].
- --reverse_read_identifier
- This is the string identifying the reverse reads. [default: 2:N:0].
Output:
A new folder with two fastq files: forward_reads.fastq and reverse_reads.fastq
Extract reads from an interleaved file:
extract_reads_from_interleaved_file.py -i $PWD/reads_to_extract.fastq -o $PWD/extracted_reads