Understandig of some bbmerge command line settings

Understandig of some bbmerge command line settings

0

Hi,

In the bbmerge documentation there are two pairs of the parameters:

  1. minoverlap and minoverlap0

minoverlap=12        Minimum number of overlapping bases to allow merging.

minoverlap0=8        Overlaps shorter than this will not be considered.

  1. mininsert and mininsert0

mininsert=35 Minimum insert size to merge reads.

mininsert0=35 Insert sizes less than this will not be considered.

I’m a bit confused with the differences of the parameters meaning within each of the pairs. E.g. to me the meaning of minoverlap and minoverlap0 is similar. Could you please explain the difference in meaning between the minoverlap and minoverlap0 and between the mininsert and mininsert0 for me?


software


amplicons


bbmerge

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