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Old 12-02-2018, 04:59 AM   #1
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Location: London, UK

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Question bbduk useshortkmers - no documentation

I am following an Illumina recommended pipeline which includes the bbduk option "useshortkmers=t". This option is not referenced in the bbduk docs, or the -h. Google only finds examples of it being invoked - with no explanations other than it conflicts with maskmiddle. I have tried with and without the option which appears to make no difference. I am curious to know if it is redundant and if not, what it does. Does anybody know? Thanks!
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Old 12-07-2018, 09:10 AM   #2
Location: Beltsville, MD, USA

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Looks like a flag from an older version of bbduk/bbduk2 that was used with mink to look for shorter kmers at the read ends.
lmolokin is offline   Reply With Quote

bbduk, useshortkmers

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