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Clair3 does not call 16 bp at each end of a reference sequence (https://github.com/HKU-BAL/Clair3/issues/257)
Supplement Clair3 calls with Bcftools mpileup/call?
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### Overview
We are encountering some issues in obtaining appropriate estimates of error rates; I believe these problems are coming from our new(-er) sequencing facility sending us fastq files contai…
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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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External workflows, e.g. the once from the training material, should be updated regularly. Or even better should be a linked against the training material. Maybe we can pull them down before running t…
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## Checklist before submitting the issue:
- [x] The issue is strongly related to the MiXCR software
- [x] The issue can be reproduced with [the most recent version](https://github.com/milaborato…
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I am creating a workflow that has many steps that use different tools, and I'm creating [minimal Docker images](https://github.com/Niema-Docker) for each of the tools. I was wondering which of the fol…
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**Describe the bug**
We have observed that `ivar variants` can generate false positive variant calls for genomes that contain insertions or deletions. Here is an example from a public genome that c…
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We are close to releasing our new pipeline schema which describe input parameters. Through chatting to people at BOSC 🍐 I've become aware of a project called [Bioschemas](https://bioschemas.org) which…
ewels updated
3 years ago
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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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The list of supported clades, which is written down in `mappings.csv`, was taken from nextclade-data, and contains three Delta clades: 21A, 21I and 21J. The latter two do not map to single pango linea…