Visualize Midas results

[lskatz]

Hi, I am asking this as a third party. I was wondering if you could help with Midas visualization. I want to suggest to others that they should visualize their Midas results. Is this possible?

[fbreitwieser]

Hi @lskatz , thanks for adding the feature request.

It seems the input files for pavian are either species_profile.txt (https://github.com/snayfach/MIDAS/blob/master/docs/species.md) or one of the merged files (https://github.com/snayfach/MIDAS/blob/master/docs/merge_species.md). species_profile.txt has the following format:

• species_id: species identifier
  • count_reads: number of reads mapped to marker genes
  • coverage: estimated genome-coverage (i.e. read-depth) of species in metagenome
  • relative_abundance: estimated relative abundance of species in metagenome

I'll need some example input files, and info on how to map species_id to the taxonomy.

[lskatz]

Could I propose a script similar to this one from my colleague Julie Shay? https://github.com/jashay90/scripts

[Anto007]

I would appreciate it very much if Pavian could somehow provide support for MIDAS as well as mOTUs v2 output files. I'm attaching here sample output files for MIDAS and mOTUs2 (generated with -q flag) mOTUs_new_taxonomic_profile.txt midas_species_profile.txt