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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]
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