Metaphlan 4 parameters for Mouse Gut

Hi everyone,

I’m excited to use the updated Metaphlan and Humann on my mouse gut metagenomes! My metagenomes are not sequenced super deep, so I wanted to test the effect of changing some parameters for identifying taxonomy.

Changing stat_q didn’t cause drastic changes, however I saw some posts suggesting to use ‘–bt2_ps very-sensitive-local’ for non-human samples. Is this still suggested for the updated databases that now contain more mouse MAGs?

My metagenomes are around 10-15M PE150 reads.
With default parameters, metaphlan identifies ~100 total features per metagenome.
Using ‘very-sensitive-local’ this increases to ~1000 features per metagenome.

I’m unsure which result ‘seems’ more appropriate, or how to decide which is optimal. If anyone has some experience or suggestions I’m happy to hear them. Also if there are any other recommendations of parameters that might be worth changing from defaults.

Thanks for the great tools!

Hi @cjharbort
For the mouse gut I would still keep the default MetaPhlAn parameters. I would not suggest to run local alignment with the metaphlan markers as it will produce a lot of false positives.

Great. Thanks so much for the support!