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Got an error while running a test run with provided S. aureus test samples (running locally on CentOS 7). When searching for solution online, I saw that the same problem appeared also for other tools,…
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Feature enables working with BAM file directly, instead of the typical fastq inputs.
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Discussed in https://github.com/cov-lineages/pango-designation/issues/1882 we found that del21997_22000 on GISAID is caused by IonTorrent and Nanopore wrongly base called with fewer number of nucleoti…
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Since a few labs including the Swedish public health institute is using Iontorrent for sequencing, we need to support that.
- adding feature to parse the value "iontorrent" in the .csv input file (…
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Although the field experiment/platform in submission-song.rdpc-qa [sequencing_experiment schema](https://submission-song.rdpc-qa.cancercollaboratory.org/schemas/sequencing_experiment?unrenderedOnly=fa…
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**Comments**
depends on q2-dada2 454 support
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Current proposal:
GISAID_query: T21994C, T21995C, del21997_22000 (S:Y145Q, S:H146K, S:K147T, S:N148T, S:N149K, S:K150V, S:S151G, S:ins152K, S:M153V, S:E154S says GIASID)
No. of sequences: 218 i…
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### Description of bug
Hello
I am trying to apply spades on merged fastq obtained from nanopore. I have one merged fastq file per sample.
I am probably missing something obvious here . I tried the …
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### Description of feature
@johnne is working on making a version of the CO1 database better adapted to the GBIF backbone taxonomy. When that is available, make sure it's selectable in Ampliseq.
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Server:
```
$ uname -a
Linux workstation 4.4.0-93-generic #116-Ubuntu SMP Fri Aug 11 21:17:51 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
```
dwgsim version: 0.1.12 (git checkout dwgsim.0.1.12)
…