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Hello I used kraken-biom to perfrom an abundance calculation from kraken2 taxonomic classification output.
My question is given a classification made from shotgun metagenomic reads. kraken2 can ass…
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After completing #1493, it's now time to do a bit of outreach to the community and ask all of the different members to add the `obofoundry` topic to their repos. It's pretty simple through the main pa…
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### Description of feature
Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics…
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I am attempting to assign taxonomy to Eukaryotes and repeatedly encounter an error with memory allotment, from what I can tell at least. I think it might be related to needing to use the duplicate tax…
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Write a universal, type-stable function for the 4 categories of prediction
- classification of currentCogScores from an arbitrary profile matrix (taxa, functions, unirefs)
- regression of currentC…
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Hello,
There are some inconsistencies between my HMMHit and FunctionHit results that I don't understand. Some functions that consist of only one gene/HMM file are absent from all of my bins according…
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Dear,
I am trying to simulate what analysing a shorter amplicon (V3V4 444bps) from Sequel IIe HiFi reads would give.
All files are replicates of the Zymo mock community V1V9 full length amplicon.
…
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Dear CT2 team,
I get the contig taxonomic classification from ```*blastx.out```, for example:
> contig1 Viruses; Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviri…
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For various reasons it would be ideal to have at least some basic taxonomic online editor for datasets in the Clearinghouse. Consider what is needed and how feasable this is with existing resources.
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I have been working on removing species to get a more manageable list of papers. For now we are removing crops and ornamental species, and monocots (although, we might add them back in later).
Dan …