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HRGV / phyloFlash

phyloFlash - A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.
GNU General Public License v3.0
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SSU from single genomes #163

Open timyerg opened 2 years ago

timyerg commented 2 years ago

Hello! Thank you for the tool. I have shotgun data from single isolates and assembled genomes (SPAdes for isolates). My goal was to extract rRNA from assembled genomes, but now I saw this tool and wonder if this tool is a more suitable for that purpose then extract from assemblies. Could you please clarify:

  1. Can I use it for single isolates rather than metagenomes?
  2. Can it deal with potentially new genera (not sure how it will match with Silva db)?
  3. If I will get several rRNA copies from single isolate, how I should deal with them? Thanks