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increase BWA sensitivity

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
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updated by h.mon h.mon • written by sacha sacha

I would like to align more reads

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

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written by GenoMax GenoMax

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

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written by WouterDeCoster WouterDeCoster

1 answer

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

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written by h.mon h.mon

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