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  • BLAST comparison of 16S rRNA against the SILVA database

    I'm currently running metagenomics pipeline through galaxy, and at the taxonomic mapping step I use ncbi blast+ wrappers to blast against a locally installed nt database. But ncbi nt database contains many data which are not totally relevant to metagenomics , so I want to locally install a more curated database like Silva or greengenes. But is it possible to do a megablast using blast+ wrappers against the silva or greengenes database? I have no idea of how to proceed. Any feedback or alternative suggestions are much appreciated.


    Thanks a lot.

  • #2
    IMO blast is a very poor solution for assigning taxonomy to 16S reads. The proper way would be to do this in QIIME or mothur. I think QIIME now defaults to uclust for taxonomy assignment (it was previously RDP classifier). Not sure about mothur..
    savetherhino.org

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    • #3
      Originally posted by rhinoceros View Post
      IMO blast is a very poor solution for assigning taxonomy to 16S reads. The proper way would be to do this in QIIME or mothur. I think QIIME now defaults to uclust for taxonomy assignment (it was previously RDP classifier). Not sure about mothur..
      Thanks I will look into that.

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