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I was looking at the function making the silva_species_assignment_v138.1.fa.gz file from SILVA_138_SSURef_tax_silva.fasta.gz.
I noticed that since only sequences with 7 taxonomy fields are chosen, s…
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I downloaded all non-_K. pneumoniae Klebsiella_ data from v0.1.
I used the equivalent of the v0.2 species_calls.tsv.gz file to identify all _Klebsiella._ I then stripped out the species I didn't wa…
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Dear dada2 enthusiasts,
I'm pretty new to dada2 so I would like to hear some opinions from those who are experts and use dada2 regularly about my issue analysis.
I have tried using filterAndTrim…
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Hi!
I am currently using PhaGCN2.3.0 for phage classification. I have previously used PhaBOX on geNomad classified viral contigs with length filter of 3000 bp (I will later only take the prediction…
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**- [X ] I checked and didn't found a related issue,e.g. while typing the title
**- [X ] ** I got an error in the following rule(s):** ` `**
Error in rule classify
jobid: 109
input: geno…
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Hi,
Any chance of producing the results, i.e. abundance and taxonomy assignment, in BIOM format?
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**Comments**
This would be nice to fix because sometimes we may want to merge closely related data. For example, it would be useful to be able to use `qiime metadata tabulate` to compare taxonomy ass…
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Hi,
I wish to add additional taxonomies to imtornado, such as GreenGenes and UNITE. As well as adding alignment models.
From the _tornado-params.sh_ parameters file, there are the following instruct…
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## What is the goal of this issue?
We currently use the rewrite slugs instead of the post type or taxonomy slugs to build the direct URLs to the relevant sections in the settings, e.g. `/wp-admin/ad…
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`assign_taxonomy.py -m uclust` (the new consensus-based taxonomy assigner) should throw an error (or at least a warning) if aligned sequences are supplied via `-i`.
This issue [recently came up](http…