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Hello,
I'm running uncalled_map with 60 threads on a 100Kb long reference and I'm observing the run-time is approximately 10X higher if average signal length is 500 instead of 1000. Adapters are tri…
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Hi,
I am getting some funky results from the sourmash gather command. I am plotting the results of the csv that gather outputs, but when I sort the values by 'gather_result_ranking' I get a plot t…
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My BWEEMS friend Anamica (https://github.com/NankaBD) is looking for support with the following problem:
"Is anyone here familiar with PacBio raw reads? I am struggling to understand how to downloa…
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### Description of feature
Centrifuge is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples, with better sensitivity than and comparable accuracy …
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Hi,
I want to calculate the abundance with reference genomes by agamemnon for metagenomic samples. In our reference database, each fasta file has a GTDB taxonomy without the NCBI Accession Number. …
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Can I expect the tool to work if I use incomplete draft genomes or MAGs as inputs? What if I use collections of CDS sequences rather than assemblies?
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Hello developers!
Im having a strange issue with rrarefy that I cant seem to figure out. At first, I thought it was a problem. I have a count table that is 77x10493 (samples are row names and vContig…
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Let's add a bulk annotation feature for protein sequences. Just like `bakta_db` we could add an entry point to provide a dedicated interface.
Entry point: `bakta_batch`
Parameters:
- `` as a meta…
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## Bug Report
Hi GATK team,
I've just been running some variant calling benchmarks on a set of bacterial isolates and I was trying to understand how GATK HaplotypeCaller chooses which re…
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Dear PANDA team,
Thank you very much for providing such amazing package.
I came across an issue in testing the HOME module incorporated in the package.
When I ran Simulation and Empirical appli…