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liu-congcong / MetaDecoder

An algorithm for clustering metagenomic sequences.
GNU General Public License v3.0
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Adding archaeal specific marker genes? #11

Closed Kohtzanth closed 1 year ago

Kohtzanth commented 1 year ago

Hello,

I was wondering if it might be possible to expand the set of 107 bacterial marker genes used in the current version to also include archaeal marker genes? like those used by the GTDB or found here: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0077033 This might improve the use of metadecoder in samples with mixed archaea and bacteria.

Thank you

liu-congcong commented 1 year ago

Hello Kohtzanth,

Thanks for the suggestion. A part of the bacterial markers in MetaDecoder is also present in archaea. Although it is not very accurate, it is possible to classify archaea. The seed selection model in the current version of MetaDecoder limits the possibility to extend the marker gene set. I already have new plans, as you mentioned. This may take a while and luck. Finally thank you very much for your advice and I hope that the imperfect program will give you perfect results.

Best,

Cong-Cong