bbduk: quality filtering and singletons

Question

[rororo]

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

Answer 1

[GenoMax]

If by singletons you mean removal of a read from R1, if the corresponding read from R2 was discarded, then yes. Trimming paired-end reads together keeps the reads in sync in both files.

Note: There is another tool called repair.sh that can fix files that you may receive that have reads out-of-sync.

[rororo]

this, plus if there is a read present in R1 but the corresponding one is missing in R2

[GenoMax]

See my edit to the post above. It will not happen as a part of bbduk.sh run.