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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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With the duplication resolved #13 we can now move forward to trimming the raw data accordingly.
### fastp
Fastp is readily updated and has good documentation and not to mention the most efficient …
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**Description**
**Sub-lineage of:** JN.1.16.1
**Earliest sequence:** 2024-6-24, Senegal
**Most recent sequence:** 2024-6-25, Senegal
**Continents circulating:** Africa (2)
**Countries circulating…
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Hello,
I'm trying to use roast in order to project alignments of 30ish plant species.
I get the error 'inconsistent row size' and afterwards that the corresponding multiz command has failed.
An exa…
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Hello,
I am trying to align some Pacbio reads using this command, after having built the index:
` minialign -l ref_index.mai SubPacbio.fq > out.sam`
This returns
```
*** Error in `minia…
ghost updated
6 years ago
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Directory ./ already exists. Writing into existing directory..
mkdir: cannot create directory ‘.//SCASA_testscasaHNVC02_20230414001259/’: File exists
Preparing for alignment..
Indexing reference.…
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Hello,
I am working with human mtDNA. When I assemble it the circularized version starts from the random positions (like 6789, 7345 and so on splitting the mtDNA in the middle) with respect to the …
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**Description**
**Sub-lineage of:** KP.3
**Earliest sequence:** 2024-3-9, Tasmania — EPI_ISL_19140364
**Most recent sequence:** 2024-6-16, Canada, Alberta — EPI_ISL_19222338
**Continents circulati…
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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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For pathogens and host genotypes, many natural variants occur and for these, we want to capture the differences to some nominally WT variant. We need to be able to distinguish when a variant is na…