Understandig of some bbmerge command line settings
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10 months ago
Denis ▴ 230

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 • 562 views
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@Brian (author of BBMap) may be the only person who can authoritatively explain those.

That said, you can create some test reads and try these options out. There is an order of precedence for various parameters that may only be clear by looking at code. Some of these parameters were likely put in place to serve a specific need @Brian had so they may not always be useful for the rest of us.

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Hi! Thank you very much for your explanation!