How to confirm species for seed material provided
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14 days ago
RT ▴ 370

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

genotyping • 196 views
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Entering edit mode
13 days ago

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.

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