Question

increase BWA sensitivity

2

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6.7 years ago

sacha ★ 2.4k

Hi,

I would like to remove human reads from a metagenomics NGS dataset ( fastq ). Which parameter from bwa mem can I change to increase the sensibility ? ( I would like to align more reads )
Penality score ? Gap open ? Clipping penality ?

bwa hg19 metagenomics • 2.5k views

ADD COMMENT • link updated 6.7 years ago by h.mon 35k • written 6.7 years ago by sacha ★ 2.4k

1

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You mean sensitivity, probably?

ADD REPLY • link 6.7 years ago by WouterDeCoster 47k

0

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I would like to align more reads

Will that need a decrease in sensitivity (and specificity?).

ADD REPLY • link 6.7 years ago by GenoMax 147k

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@sacha Don't think there is a reason to delete this thread...?

ADD REPLY • link 6.7 years ago by WouterDeCoster 47k

score 2 · Accepted Answer · 2018-03-28

2

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6.7 years ago

h.mon 35k

Personally, I would use the RemoveHuman approach from BBMap.

Are you trying to clean Illumina reads? BWA is already pretty sensitive, you will probably increase false positives if you tweak the parameters. If you want increased sensitivity, with (I believe) the same precision, you can try vg:

VG_graph

ADD COMMENT • link 6.7 years ago by h.mon 35k