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 ? 






Personally, I would use the [RemoveHuman][1] 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][2]




  [1]: http://seqanswers.com/forums/showthread.php?t=42552
  [2]: https://cloud.githubusercontent.com/assets/145425/24107859/370225f6-0d8c-11e7-8af4-ab9250971ec8.png