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I've run modified base calling using `Dorado` which generated a BAM file with MM/ML tags. Since `Dorado` does not do trimming I had to convert BAM to Fastq and then ran `NanoFilt` to trim the reads. N…
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Hi,
Thank you corecruncher
I have been using corecruncher with (auto) prokka translated protein sequences with aligner muscle (v3.8.31) which fails but mafft goes to completion. So, perhaps the …
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Hi,
I am trying to run bambu with the following code:
se.quantOnly
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Hello,
Is there a way to specify additional flags/options when submitting a PECAT job on a computing cluster? For example, I would need to include some required information specific to my universit…
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Hello,
I am running PECAT v.0.0.3 to correct reads on a SLURM cluster. Here is my config file.
```
project=Emac_PECAT
reads=/vscratch/grp-tkrabben/MacGuigan/rawNanoporeData/Emac/Emac.cell1.pas…
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I don't think a proper query can be made to exclude everything else, given the fact that new separate lineages are popping up from time to time.
![image](https://github.com/sars-cov-2-variants/lin…
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For generating the "raphgraph" plot, we are using a combination of Genbank data and VirusSeq data to extract the frequencies of mutations for specific variants of concern; see https://github.com/CoVaR…
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Draft content for block 3 of the workshop.
This is the superset of issues #27, #28, and #29.
### Data
- Workshop data available [here](https://www.dropbox.com/scl/fi/gse156zgu4sl5u86s21on/L…
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When methylation tags are supplied along with hard clipped CIGAR strings the methylation tags are rendered useless as they the counting of total canonical bases is no longer possible. It appears as th…
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### Description of the bug
Hi,
I recently run sarek with the UMI pipeline for WES data, it successfully finishs but only performs alignment and does not perform variant calling.
For the UMI pipelin…