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I am attempting to basecall using dorado, and I had a question regarding which kit I should provide as part of their `--kit-name` flag when using `dorado basecaller`.
In my library preparation, I …
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Hey folks, big fans of starcode. I really like this tool (well designed, Levenshtein distance, code is readable), and I'd like to use it for all my seq clustering needs. I hope y'all are continuing ac…
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Dear,
I find the ANCOM-BC approach to identify deferentially abundant taxa very interesting and was wondering if the estimated sample-specific offset term could be replaced by a known sampling frac…
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I uploaded the [example data](https://github.com/loculus-project/example_data/tree/main/ebola_zaire) for ebola zaire (which we may be out of date) and found preprocessing stalled. When looking at the …
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I am analyzing ITS1 amplicon data using DADA2 and the UNITE reference database. Last week I had an issue where the assignTaxonomy function was labeling ASVs as outlandish taxa (telling me I had marine…
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Hello!
I am trying to run readfish with Icarust and I cant seem to fix this error:
2024-05-30 17:49:24,430 readfish /home/user/miniforge3/bin/readfish targets --port 10000 --toml test.toml --device…
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Hi all,
I am using DADA2 to analyze 13 biofilms samples sequenced for the 16S rRNA V4 region.
The samples were sequenced in two different periods. In detail 12 samples are sequenced together and 1…
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Hello,
I have followed the BaitSTR workflow to create 'contigs.str.fa' for one of my datasets. I am now trying to use BaitSTR_type and it looks to be getting hung up on creating an index. I think …
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VPIPE_BASEDIR = /opt/V-dock/V-pipe/workflow
Importing legacy configuration file vpipe.config
MissingSectionHeaderError in line 107 of /opt/V-dock/V-pipe/workflow/rules/common.smk:
File contains no …
dstcr updated
2 years ago
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We want to use lotus2 to analyze ITS sequences. A common issue is the read-through into the opposite primer as described in the dada2 toturial: https://benjjneb.github.io/dada2/ITS_workflow.html
Can …