# Include Genome Sequences in PanPhlAn3 **URL:** \ **Category:** PanPhlAn\ **Created:** [April 22, 2021, 7:26pm UTC](https://forum.biobakery.org/t/include-genome-sequences-in-panphlan3/1991 "2021-04-22T19:26:14Z")\ **Posts on this page:** 1\ **Showing post:** 4
**Author:** ![leonard.dubois](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/leonard.dubois/32/750_2.png) [@leonard.dubois](https://forum.biobakery.org/u/leonard.dubois)\ **Post date:** [April 26, 2021, 3:49pm UTC](https://forum.biobakery.org/t/include-genome-sequences-in-panphlan3/1991/4 "2021-04-26T15:49:00Z")
> (we have recovered isolates from fecal samples for species which were not detected by PanPhlAn3 [presumably due to low coverage/abundance]). Maybe this can be due to parameters tuning of strain detection, in this topic we discussed this kind of issue : > [@PanPhlAn threshold selection](https://forum.biobakery.org/t/panphlan-threshold-selection/1748): > > Dear Developers, I am working on PanPhlAn recently. And I have a few questions about the choice of thresholds, especially about “left\_cov” and “right\_cov”. I attached my current procedures below, along with questions. Thank you in advance for your patience. (1) It seems to be necessary to select the threshold in a species depend manner. Below are a few examples. They are scatter plots of left\_coverage and right\_coverage (intermediate output of PanPhlAn, normalised by median coverage.) If that still does not work, the last method you mentioned (“Eg. aligning every ORF to the PanPhlAn species database instead”) In the topic linked above, I explain how the coverage threshold work and the kind of profile PanPhlAn expect from a natural microbiota sample. I’m not sure making a fq file out of the genome will be treatable by PanPhlAn, as house-keeping genes present in other species are expected at very high coverage while parts of the accessory genome should have a low coverage compared to the rest of the species genome. --- _[View the full topic](https://forum.biobakery.org/t/include-genome-sequences-in-panphlan3/1991)._