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bbduk: quality filtering and singletons
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3.0 years ago
rororo • 0
@rororo37162

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
bbmap genome reads • 581 views
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3.0 years ago
genomax 68k
@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.

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

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

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