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BinSPreader to refine MAGs from vamb using individually assembled samples #1023

Answered by asl
eperezv asked this question in Q&A
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Well, BinSPreader relies on assembly graph and in your case there is no single assembly graph to use for the refinement. I must also note that the co-binning procedure might lead to the high duplication ratios in MAGs especially if multiple strains are present. So, likely your only way is:

  • Co-assemble everything
  • Take the scaffolds from this co-assembly
  • Bin them and using BinSPreader for the refinement

Alternatively:

  • Assemble your samples individually
  • Bin individual samples separately
  • Use BinSPreader to refine them
  • Use DAS_Tool / dRep to dereplicate MAGs. Be careful as the tools might drop short contigs that come from the elements you've interested in

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@eperezv
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@asl
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asl Jun 30, 2023
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