Scripts for metagenomics analysis
trimgalore.shscript for read trimming, runs as a slurm array, samplesheet required as input, expected output are trimmed reads and a new samplesheet. Depends onsamplesheet.shscript ingithub:jamesboot/utilitiesbwt2_pe_host_depl.shscript for host read removal using bowtie2, paired end reads. Requires the output fromtrimgalore.sh