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donovan-h-parks / RefineM

A toolbox for improving metagenome-assembled genomes.
GNU General Public License v3.0
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Questions about Removing contamination based on taxonomic assignments #15

Closed Feverdreams closed 6 years ago

Feverdreams commented 6 years ago

Hi Donovan,

I am trying to filter scaffolds following the methods presented on your paper (Parks DH et al. 2017. Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life). However, I am not sure that do I have to process the database downloaded from RefSeq GenBank56 release, or simply use the database you provided.

Also, is the step of filtering scaffolds with incongruent 16S rRNA genes involved in the function of Removing contamination based on taxonomic assignments of refinem? I mean, does the refinem filtering scaffolds with incongruent taxonomic classification or incongruent 16S rRNA genes all by "refinem filter_bins taxon_filter.tsv" ?

Could you give me some suggestions about it?

Thanks a lot.

Looking forward to your reply.

Regards, Edward

donovan-h-parks commented 6 years ago

Hello. I would recommend using the database and taxonomy file I have provided. The "Removing contamination based on taxonomic assignments" is not specific to 16S sequences. I am still working on a public database and documentation for identifying incongruent 16S. I hope to have this done in the next day or two.

donovan-h-parks commented 6 years ago

I found the time to put the 16S rRNA database together this morning and to write up some brief documentation on the RefineM GitHub page.

Feverdreams commented 6 years ago

Thank you so much!

Edward