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If a user want to check mutation frequencies for all Sublineages of a Lineage one should be possible to use Lineage.*
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The documentation for VOCAL details nicely the use of the `selector.py` function to generate a table of mutation that is VOCAL compatible from a covsonar match table (VOCAL tool/Ecosystem section)
…
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I suggest using the poreCov pipeline as the backend for SARS-CoV-2 wastewater lineage deconvolution from nanopore long reads. You already added `freyja` ( #274 #270), which is great as the current com…
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It would be great if covsonar 2 was faster than covsonar 1, but we don't expect that to be the case because covsonar 2 is much more flexible than 1. Nevertheless, covsonar 2 has to be fast enough to b…
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The following covsonar 1 commands are commonly used and need to be supported by covsonar 2 if we are going to transition to using it. To be marked as completed, the command needs to be tested to ensur…
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Hey there,
It would be wonderful to have the option to match multiple accession IDs from a list:
```
path/to/covsonar/sonar.py match --acc --file myids.txt
```
with one accession per line in `m…
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If you create a new database with a property for lineages, and add some sequences with lineage metadata, you will get zero results if you do a sublineage search (e.g. `match --LINEAGE "B.1*"`) before …
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the options `--only_frameshifts` and `--no_frameshifts` would be cool for covsonar2.
They work in version
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A weird error, maybe due to my covsonar installation.
```bash
python3 /scratch/hoelzerm/git/covsonar/sonar.py match --db rki.db --date 2021-12-07:2021-12-07 --tsv > out.tsv
```
If it is not r…
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Before making covsonar 2 the stable release, we need to be certain that the mutation profiles that both tools produce are either the same, or that the differences can be explained and that covsonar 2 …