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contig-level coverage is already generated and provided for individual samples, but that would only include the MAGs from that sample
should make a combined bowtie2 db of all MAGs and then map each sample to that to get MAG coverages across all samples
note that this would be dividing coverage/abundance estimates between closely related MAGs recovered from different samples. So a dRep step may also be wanted, then making a dRep'd MAG bowtie2 db for mapping...
or maybe just providing a skani/ANI output for all MAGs and leaving mapping to all...
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AstrobioMike
changed the title
capture and report MAG coverage across samples with metagenomics workflow
[Metagenomics wf] capture and report MAG coverage across samples
Jun 21, 2024
The text was updated successfully, but these errors were encountered: