Using strainphlan with long reads?

Microbial community profiling StrainPhlAn
1

Hello,

I was wondering whether strainphlan will work with a long read dataset? Is there a way to use minimap2 for mapping to the metaphlan database?

Thank you

2

Hello,

in the next release of MetaPhlAn/StrainPhlAn 4.2 there will be a support for long reads in both tools using minimap2 as the mapper. It should be released within few weeks or months. If you’re eager to try it immediately, you can install the development version from the branch “code_refactor” GitHub - biobakery/MetaPhlAn at code_refactor . I recommend installing the “standard” version via conda to get metaphlan with all the dependencies and then via pip install the development version over it. Then you can run metaphlan on your long read dataset and use the SAM files as input for sample2markers and Strainphlan. If you do so, we’d like to hear your feedback as this will help us to improve the long read support in our tools.
Best
Michal