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Currently, we have [five samples](https://github.com/dhimmel/fratjuice/blob/2bf8530921bb3921700cfc8e61b15e88bd85de64/samples/samples.tsv). Each sample is in either a 15 or 50 mL conical-bottom tube. S…
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Hi,
I am using this pipeline to reanalyze some data from Illumina Novaseq PE250bp.
And I have noticed that in this paper , they sequenced at Hiseq PE250bp (McNichol, J., Berube, P., Biller, S.…
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I'm working on a generalizable pipeline for metagenomics that has bacteria, archaea, eukaryotes, and viruses.
The `download_eggnog_data.py` script asks for taxonomy. Would I download each of these…
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since we're currently using the GTDB bacterial/archaeal genome database for decontamination, the automated classification approach doesn't correctly classify eukaryotes. so when cleaning eukaryotic bi…
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Found dalliance and DAS while looking around for genome browsers, and it's definitely the coolest-looking one I've found. However, despite billing itself as a general purpose genome browser, it seems…
kueda updated
13 years ago
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Hi,
I was using Bracken to re-estimate reads at Class level for Eukaryotes. Now, there is a certain fish Order that I don't want included in the general fish Class, because it's the Order of my hos…
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# Better reporting of removed genomes
If an automatic phylogenetic tree is produced via GToTree, it's possible that some low-quality genome sequences will be filtered out by GToTree during tree const…
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It would be good for users to have an easy way to turn markers on and off when running PhyloSift. I suggest we could do this as command line flags, because I think people will get annoyed if they have…
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Would be useful to give quick visual summary of what organisms are collected in the alignment.
One option: represent aligned sequences in a tree or simply a bar-chart, colored by species membership…
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# List of expected functions from [`molevol_scripts/R`](https://github.com/JRaviLab/molevol_scripts/tree/main/R)
Ensure all functions are present and accounted for. Use list depth to determine if f…