# Help with workflow

**URL:** <https://forum.biobakery.org/t/help-with-workflow/2242>\
**Category:** StrainPhlAn\
**Created:** [June 11, 2021, 10:35pm UTC](https://forum.biobakery.org/t/help-with-workflow/2242 "2021-06-11T22:35:29Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![Ana](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/ana/32/841_2.png) [@Ana](https://forum.biobakery.org/u/Ana)\
**Post date:** [June 11, 2021, 10:35pm UTC](https://forum.biobakery.org/t/help-with-workflow/2242/1 "2021-06-11T22:35:29Z")

</div>

I have raw read files (2 fastq files per isolate; over 100 isolates) and I want to make a tree from them.

I’ve tried with metaphlan2 and metaphlan v3 but I can’t get a work flow… so many error at every step. Do I even need to use sample2markers? Maybe there’s issues because I am using a Mac? Can someone write out a simplified step-by-step protocol.

---

<div class="post-metadata">

**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\
**Post date:** [June 14, 2021, 7:42am UTC](https://forum.biobakery.org/t/help-with-workflow/2242/2 "2021-06-14T07:42:31Z")

</div>

Dear @Ana  
Thanks for getting in touch. StrainPhlAn (as well as MetaPhlAn) is designed to work on metagenomic data. While it could be possible to use StrainPhlAn to reconstruct the phylogeny of your isolates using the RAW reads (if all belong to the same species), it is not the most appropriate / suitable solution.  
My suggestion for you, is to assembly your isolates (e.g. using SPAdes: [SPAdes – Center for Algorithmic Biotechnology](http://cab.spbu.ru/software/spades/)) and then run PhyloPhlAn 3 on the assembled genomes ([https://www.nature.com/articles/s41467-020-16366-7](https://www.nature.com/articles/s41467-020-16366-7)). If you have any problem running PhyloPhlAn, here is the forum: [PhyloPhlAn - The bioBakery help forum](https://forum.biobakery.org/c/microbial-community-profiling/phylophlan/13)

Best,  
Aitor

---

<div class="post-metadata">

**Author:** ![Ana](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/ana/32/841_2.png) [@Ana](https://forum.biobakery.org/u/Ana)\
**Post date:** [June 14, 2021, 8:37pm UTC](https://forum.biobakery.org/t/help-with-workflow/2242/3 "2021-06-14T20:37:13Z")

</div>

Thank you for the reply. What about a workflow using SNP’s? How would I do that?

---

<div class="post-metadata">

**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\
**Post date:** [June 15, 2021, 8:53am UTC](https://forum.biobakery.org/t/help-with-workflow/2242/4 "2021-06-15T08:53:23Z")

</div>

PhyloPhlAn phylogeny is based on SNPs in core genes (at the species level) or in universal marker genes (at the genus level and below). After assembly your reads (here a really nice guide [De novo genome assembly](https://astrobiomike.github.io/genomics/de_novo_assembly)), there are available a lot of tutorials you could follow: [GitHub - biobakery/phylophlan: Precise phylogenetic analysis of microbial isolates and genomes from metagenomes](https://github.com/biobakery/phylophlan#tutorials)