Run this pipeline to get initial quality control for new sequence lanes.

This can be done by running

wget ftp://ftp.ensemblgenomes.org/pub/plants/release-27/fasta/zea_mays/dna//Zea_mays.AGPv3.27.dna.genome.fa.gz

on most unix systems. You may need to use curl instead on a OSX.

Move the reference into the data directory and rename as ref.fasta.gz (keep the reference gzipped). Then run:

sbatch -p <queue> ref.sh

This will index the reference for you.

For quality control, then run:

while read r1 r2; do sbatch -p <queue> qc.sh $r1 $r2; done < list.txt

Where list.txt is a file with the full path to read1 and read2 on a single line separated by white space. If you have multiple lanes you want to run simultaneously, then each line of the file should have read1 and read2 separated by white space.

Ideally this should be run on gzipped fastq files.

The script will create a directory of summaries named after each file in the results directory, with an html output called fastqc_report.html in each directory. The initial quality report will also list over-represented sequences, which should include adapters if there is considerable adapter contamination.

Run with test_r1.fastq.gz and test_r2.fastq.gz