Silas Kieser

Feature request: mmseqs createhdf

1

As the data that can be processed with mmseqs is generally quite large. The tsv output is usually very large. I wonder if it would be difficult to create hdf...

createdb out of memory

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## Expected Behavior createdb creates db without error ## Current Behavior created command is killed after 261 mio genes on a node with 500gb memory ## Steps to Reproduce (for...

new dependencies for atlas 2.11

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Describe your pull request here m ---- Please read the [guidelines for Bioconda recipes](https://bioconda.github.io/contributor/guidelines.html) before opening a pull request (PR). * If this PR adds or updates a recipe, use...

Subroutines for classify

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I had some bad experiences with gtdb-tk classify which I run on large datasets. - For example, It passed all the steps but then failed because the symlinked files already...

`atlas init-public`doesn't work.

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Unfortunately I based this part on scripts that interact NCBI Trace, which was discontinued in June 2022. Apparently it is very complicated to get the right data from NCBI. I...

Test for cobining

I got almost zero mapping rate for a human dataset. In addition the minsites limits the alignment to 10 sites so ambiguous reads are discarded.

Older data with read length 50 is eliminated with default min read length 51.

Host contamination in final bins

4

Question from @botellaflotante For some reason I have some host contamination within the MAGs. But maybe I could filter that with MAG purify on the bins and rerun genomes... Do...