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