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franciscozorrilla / metaGEM

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
https://franciscozorrilla.github.io/metaGEM/
MIT License
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[Question] Option to filter host's DNA #27

Closed matrs closed 3 years ago

matrs commented 3 years ago

Hello, I was wondering if you haven't tried to check for host DNA in the input files. I've seen some reports showing that it can be problematic for downstream analysis. I'm new analyzing metagenomes, so I'm not sure about it and maybe for your particular analysis this isn't a concern. Searching for software to do this, I found kneaddata, which separates bacterial DNA from host DNA, although it seems to include trimming too, which maybe isn't the most convenient.

https://huttenhower.sph.harvard.edu/kneaddata/

Jose Luis

franciscozorrilla commented 3 years ago

Hi Jose,

Thank you for your suggestions, KneadData or something similar may be a good addition for user cases where removing contaminants is imperative for analysis. Btw, if you want to filter out eukaryotic DNA you can also run EukRep on your assebmlies as shown here or see #14 . Having said that, KneadData would still be useful for removing eukaryotic reads from humans or other species.

Francisco

matrs commented 3 years ago

I see, that information about euKRep it's useful, I'll check it.

Thanks!