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Here is an outline of a workflow that needs to be enabled in Galaxy to allow variant calling on HIV-1 datasets
- [ ] Upload all datasets for `PRJNA517147`
- [ ] QC with `fastqc` and `multiqc`
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I'm running metaviral SPAdes with low-complexity (2-5 viruses) samples, and while it successfully works with most of them, three of them are consistently failing without warnings. The logfile reports …
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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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**Description:**
Three sequences are from a chronic patient, and one is from a separate patient. All sequences have substantial differences. I'll list the mutations for the separate patient, but give…
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We've had reasonably good results with [IVA], but it has a few problems:
1. Some samples are very slow, even taking multiple days. Random primers seem to be slow.
2. We find contigs with a lot of …
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Proposal for a sublineage of BA.4.1.9
Earliest sequence: 20.03.2023 (Spain)
Countries detected: Spain
Defining Mutations:
nuc unique A761G, C874A, T3508C, C5184A, C6336T, C6726T, C22571T, C29200…
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Helllo
My name is Andrea, and I am currently working with a set of SARS-CoV-2 sequences obtained by Illumina tech in order to find different SNVs that lead to the identification of viral quasispec…
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### Expected behavior
**TL;DR**: I want a (mostly) unambiguous pair of terms to rename the types `Variant` and `Variation` to. I chose "Haplotype" and "Variant," but want feedback from other biologis…
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Hello, my name is Andrea.
I am trying to use the HaplotypeExplorer tool in order to study some quasispecies sequences that proceed from the same sample. Specifically, I am trying to run this script …
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Hello.
My name is Andrea, and currently I am working with SARS-CoV-2 sequences in order to identify quasispencies within the samples that I study. I've been trying to use lapis.cov-spectrum.org in o…