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Deer developer,
I still don't understand the relative abundance calculation in CoverM. Whether the result of CoverM is the percentage of mapped reads of each genome ? I just want to get `the…
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Hi, developer,
I am confusing about the ssu_finder in CheckM. I have used RefineM to filter thedivergent genome properties, Removing contamination based on taxonomic assignments, incongruent 16s in…
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I recently installed RGI via bioconda. I can't find a version command for rgi itself, but I'm guessing this must be version 5.1.0.
I tried out RGI on a 3rd-party genome sequence from NCBI (https:…
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Hi,
I would like to detect selective sweeps in a set of bacterial genomes, and RAiSD seems as a perfect tool for it. But I have a question about the input vcf file I should use to run RAiSD.
The…
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Hi,
I have noticed that many bacterial MAGs [generated](https://www.biorxiv.org/content/10.1101/762682v1) seem to have highly fragmented genomes (~200 contigs on average), so I am trying to implem…
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This file contains the definition of the MAG class, which is basically a subset of the contigs in a metagenome. The issues that I came across are outlined below:
1. [x] The name of the script and t…
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Apologies if my request is misplaced here. I see the TSV outputs were available in v3, with JSON being the preferred output format for v5
I am looking for a simple script which can parse the antiSM…
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Hi!
Thank you for Phanotate, the tool is really useful and easy to use. I've been using it for my own work, and I was wondering what is a safe cutoff for selecting the ORFs predicted by Phanotate?
…
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# sourmash / kmer approach implementation
* not sure about the quality but I want to test this
## database
* we need to pre-build a phage DB @stormrider can you link collect DBs for this and repo…