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I am starting out in metagenomics,

Aim I wish to understand the whole analysis from the raw reads to interpretation.

Background My current pipeline is used for:

  • analyzing human gut microbiota cleans reads,
  • filters out human genome, and
  • maps the reads to known microbial species using IGC and mOTUs.

Question I am looking for basic tools to visualize the output, in order to get some biological and statistical insights (Linux and python are preferable environments).

For example, an obvious step would be to display the mOTUs analysis results on the phylogenetic tree, using the full phylogeny provided with this package. Whilst I could implement it myself, I was wondering if anyone else had previous experience?

Update
One package that I found useful is MOMR (through in R).

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