I want to use bbduk of the bbmap package to quality filter my paired-end Illumina reads according to the following:
- minimum quality value of 2
- minimum length of 36
- remove single reads
To me, the bbduk manual is here a bit unclear. Does the following command remove singletons?
bbduk.sh in1=R1.fq in2=R2.fq out1=R1.clean.fq out2=R2.clean.fq trimq=2 minlen=36