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**Context**
TREETime is a computational bottleneck in the Augur bioinformatic pipeline, especially when modeling thousands and thousands of raw genomic data.
Bottom line up, how to have Augur ab…
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A living google doc describing the form and function of different helicases, including the SARS-CoV-2 helicase, Nsp13.
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* There are 16186 cases where a term has the proteoform notation on both the definition and the PRO-proteoform-std lines.
* There are 944 non-obsolete cases where a term has the proteoform notation o…
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Dear developers,
Thanks so much for providing VIGOR4 which is a very convenient software for virus annotation, especially for SARS-CoV-2.
But can i suggest adding a new databse of coronavirus in v…
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I assume something like:
```
planemo run #workflow/github.com/iwc-workflows/sars-cov-2-pe-illumina-wgs-variant-calling/COVID-19-PE-WGS-ILLUMINA ...
```
Proposed by @wm75 some time ago.
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@asl @rcedgar
To help coronaSPAdes identify CoV-associated contigs from the full assembly graph, we need to expand our set of target HMMs.
Versions:
1. Pfam-SARS model HMMs
2. (current) All H…
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Hi,
I'm trying out using `kraken2` for the first time. I have short (150 bp) sequencing reads that are ostensibly of SARS-CoV-2, but as part of QC I wish to classify them using `kraken2` to see if …
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I have just checked encodings that autotokenizer produces. It seems that for words "wuhan", "ncov", "coronavirus", "covid", or "sars-cov-2" it produces more than one token, while tokenizer produces on…
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Title: SARS-CoV-2 infects T lymphocytes through its spike protein-mediated membrane fusion
# General Information
## Please paste a link to the paper or a citation here:
Link: https://doi.or…
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I'm having problems with Longshot when running the [Artic pipeline](https://github.com/artic-network/fieldbioinformatics) (even after updating Longshot to v0.4.3, since Artic still uses v0.4.1), in th…