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[Metagenomics wf] capture and report MAG coverage across samples #24

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AstrobioMike opened this issue Jun 20, 2024 · 0 comments
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@AstrobioMike
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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...
@AstrobioMike AstrobioMike self-assigned this Jun 20, 2024
@AstrobioMike 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
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