Simulate fastq files from a list of RefSeq URLs
Given a .csv file of RefSeq asssembly URLs and read depths, and optionally a region defined in samtools faidx style, simulate fastq files at a range of read lengths.
nextflow run PenGU-testdata-build.nf [OPTIONS]
By default, submit to SLURM cluster. Change 'slurm' to 'local' in nextflow.config if you want to run locally.
--csv Input .csv file [default: 'genome_urls.csv']
--refreads SRR accession of a readset from a similar sequencer. Used for generating quality scores [default: 'SRR8062313']
--fq_header String including "@" in fastq header [default: '@M04531:123:000000000-T3STP:1']
--read_lengths Comma-delimited list of read lengths to simulate reads at [default: '125,150,175,200,225,250']
--outdir Output directory [default: ./output]
Requires an NCBI_API_KEY.
Set export NCBI_API_KEY=0123456789abcdef somewhere in your environment (like ~/.bash_rc).
This pipeline contains GPLv3 licensed code from ArtificalFastqGenerator.