Help with workflow

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.

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) and then run PhyloPhlAn 3 on the assembled genomes ( If you have any problem running PhyloPhlAn, here is the forum: PhyloPhlAn - The bioBakery help forum


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

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), there are available a lot of tutorials you could follow: GitHub - biobakery/phylophlan: Precise phylogenetic analysis of microbial isolates and genomes from metagenomes

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