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### Context
To support running ingest on Terra, we need to support downloading existing Nextclade alignments and metadata from remote storage other than AWS's S3.
### Description
We need to suppo…
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Hello,
I have been using Pangolin to evaluate my tool on a simulated dataset.
However, I cannot get the lineage that I expect with pangolin. I would be glad if you could have a look why that cou…
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I have been running a bunch of viruses in parallel using --no-longshot from the same directory. Medaka appears to very briefly have a tmp file that is not uniquely named (tmp.medaka-annotate.vcf), and…
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## Context
In the near future, we would like to support region-specific flu builds and also enable other researchers to use this repository to define their own custom flu builds in the same way [th…
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**Description :**
Long read sequences are failing in the demix step if the sequence id in the bed file is not matching with the reference.
**Sample name**: SRR21595278.fastq.gz
**Bed file**: http…
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Similar to #9 but I can't solve it with regex. I downloaded the nextstrain tree (Jan 4, 2021) for nCov and wanted to run TreeToReads.py with it (newick attached below). However the seq-gen part give…
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## Context
In a pathogen repo, there will technically be 3 separate workflows that can be run: ingest, phylogenetic, and nextclade.
It's unclear how we want to set up the standardized GitHub Actio…
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Hello everyone,
New user here. I have been trying to run artic pipeline here.
Right after align_trim, I get lines and lines of error message and assembly finishes. Even though I have viral assem…
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Currently there is no way to link to the latest report, and user needs to know the date:
https://nextstrain.org/narratives/ncov/sit-rep/2020-01-30
Older, reports (which users may, for example, b…
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Hi!
I was trying to get a consensus sequence using artic network bioinformatic protocol, i used the nex comand lines:
artic minion --medaka --medaka-model r941_min_high_g360 --normalise 200 --thre…