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Dear Simon,
I've been running VirSorter on the cyverse platform before, and now installed it on a server (CentOS Linux 7), as I'd like to use it for a larger number of samples. I followed the insta…
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I am running Canvas in a docker container using the hg19 reference files from the S3 link.
I am trying to call Canvas using variants called by strelka/starling on a shallow WGS (7 fold) dataset:
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I've been running vRhyme on some of my test data [SRR11140750-test.zip](https://github.com/AnantharamanLab/vRhyme/files/13515750/SRR11140750-test.zip) and vRhyme doesn't generate any output bins (alon…
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When running winnowmap, the -I option is not recognized.
e.g. after generating the repetitive_k15.txt with meryl:
`winnowmap -W repetitive_k15.txt -a -x map-pb -Y -L --eqx --cs -I 32G ref.fa.gz re…
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## Expected Behavior
Include a brief description of the database hits in the html and tabular output files from a search.
## Current Behavior
The Foldseek web server includes some functional desc…
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Dear @oushujun ,
Thank you for developing this useful tool. I have run it successfully and found that SINEs and LINEs could't be identified based on structure features. However, we didn't have such T…
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I have built custom database which contains the entire GTDB as well as unique MAGs I generated ~ 67,000 genomes. The hash.k2d is 305Gb in size. When I try and classify reads kraken2 cannot even load t…
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Hi,
We have been using SyRI for two-genome comparison in multiple species pairs, and issue #48 has been helpful in fixing problems whenever "Index out of range" error shows up. The chromosomes to re…
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Hi Shujun,
Another question. I'm running panEDTA on a bunch of species. It says it's successfully reannotating the structurally annotated TEs, e.g.:
> Sat Oct 14 15:10:05 EDT 2023 EDTA final …
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Hi,
The gtdb_to_ncbi_majority_vote.py is great but is subject to biases when multiple genomes are incorrectly annotated on the NCBI.
Have you considered implementing more complex rules such as:
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