How to confirm species for seed material provided

Question

[GR]

Hi All,

I was wondering if there is a way to confirm the species for a seed material? We don't have the correct info about the sub-species (it is one of the three). There are genomic resources available for these species. Please suggest what will be the insilico/wetlab steps to confirm this.

Thanks, RT

Answer 1

[Matthias Zepper]

Probably the fastest, quick and dirty approach is mapping to multiple references simultaneously, e.g. with BBSplit or - if there are no reference genomes available - using Seal. See the TaxonomyGuide enclosed with BBTools for more details.

A more sophisticated approach that you can consider if you plan to add more sequences/samples later is the construction of a pan-genome and using tools for graph-genome analysis.