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I have been using the PaleoDB to compile stratigraphic ranges for taxa and have discovered that it is possible for the early and late intervals returned for a taxon (when downloading taxonomic names) …
meljh updated
5 years ago
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I'm trying to use a clustered version of the NR database for taxonomy assignment but am running into some issues. Any assistance would be appreciated.
## Expected Behavior
When running `mmseqs cre…
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I would like to propose the idea for "Pipeline for customized phylogeny based on user provided gene/protein sequence(s) using Open Tree of Life data".
Suppose a researcher has newly sequenced a gene…
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This lesson is meant to be a bit modular, so that it can be adapted to a few different workflows depending on user preference. That said, we do need a default one. Here are my thoughts:
**OTUs vs. …
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Now that there is a critical mass of minor improvements to be made, I am creating a master issue to organize all of the changes which will go into a new minor release. I am describing this as a minor …
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Hi there,
I'm wondering about the assignment of BVAB(1/2/3) as you say that VALENCIA only considers species level annotation for Lactobacillus, Gardnerella, Prevotella, Atopobium and Sneathia, but…
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This is probably a dumb question, but I don't understand why when I switch output format from 6 (blast-style) to 102 (taxonomy), the number of pairwise alignments changes. I made a small sample FASTA …
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I just ran gather on some genomes (attaching a snippet of results below). These are all single genomes.
```
overlap p_query p_match avg_abund
--------- ------- ------- ---------
5.3 Mbp …
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Hello,
I am trying to build standard kraken2 database. I have used the default command:
`kraken2-build --standard --threads 8 --db kraken_standard`
The database is created without any errors but …
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Hello! I am working on a metabarcoding project for marine samples, and I am trying to build my reference database for taxonomic assignment. I would like to download all COI sequences for eukaryotes fr…