I am trying to remove human reads from my metagenomic sequences (skin samples).
I have used the command recommended in the bbmap documentation:
bbmap.sh minid=0.95 maxindel=3 bwr=0.16 bw=12 quickmatch fast minhits=2 path=/path/to/hg19masked/ qtrim=rl trimq=10 untrim -ea -Xmx100g in=reads.fq outu=clean.fq outm=human.fq threads=12
My input is Illumina HiSeq 4000 Paired-end, 2x150 bp reads, so I want to split paired-end reads back into separated fastq files .._r1 .._r2.
Is there a way to do this using BBTools?
Thanks in advance!