Question: increase BWA sensitivity
2
gravatar for sacha
2.3 years ago by
sacha1.9k
France
sacha1.9k wrote:

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 ?

hg19 bwa metagenomics • 1.0k views
ADD COMMENTlink modified 2.3 years ago by h.mon30k • written 2.3 years ago by sacha1.9k
1

You mean sensitivity, probably?

ADD REPLYlink written 2.3 years ago by WouterDeCoster44k

I would like to align more reads

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

ADD REPLYlink written 2.3 years ago by genomax85k

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

ADD REPLYlink written 2.3 years ago by WouterDeCoster44k
2
gravatar for h.mon
2.3 years ago by
h.mon30k
Brazil
h.mon30k wrote:

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 COMMENTlink modified 2.3 years ago • written 2.3 years ago by h.mon30k
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