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liaoherui / StrainScan

High-resolution strain-level microbiome composition analysis tool based on reference genomes and k-mers
https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01615-w
MIT License
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How to infer different species-level abundances based on strain-level abundances #17

Open xujialupaoli opened 5 months ago

xujialupaoli commented 5 months ago

Hi! Thanks for the clear documentation and awesome tool. I have read your explanation about Strainscan, and it seems that it is used to analyze the abundance of each strain in a specified species. But I want to analyze multiple species. Can I build a strain database from multiple species to analyze the abundance of each strain to infer the abundance of different species?

liaoherui commented 5 months ago

Hi, thanks for using StrainScan!

Currently, StrainScan can only support the strain identification for a specified species in a single run. If you want to identify strains from multiple species, one possible solution is to build multiple strain databases for multiple species and run StrainScan with all these databases. Finally, given the identified strains and their abundance, you can infer the abundance of strains of different species.

xujialupaoli commented 5 months ago

Thank you!

xujialupaoli commented 5 months ago

Can the strain information corresponding to different reads be obtained from the output results of Starin Scan?

liaoherui commented 5 months ago

Regret to say that the current version doesn't support that either. I am considering developing a new tool to support these new features (strains from multiple species + reads assignment).

However, I think Kraken2 can be used to do that even though it can have worse performance at the strain-level sometimes. But its performance at the species-level is satisfactory according to my experience. Maybe you can try that tool if required.

xujialupaoli commented 5 months ago

thank you very much!