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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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As a TL I would to check the report consistency, identify and flag inconsistencies so that we can improve confidence in the report.
**Acceptance Criteria**
- [ ] Identify report rows where the m…
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Hi,
I'm running recentrifuge with kraken2 with the main goal being removal of contaminants and for this I have negative control(s). However, what I'm seeing in my results is that the "Exclusive" and…
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@wdduncan @lwaldron @lgeistlinger @cmungall
From our conversation on Thursday (thank you btw @wdduncan, it was really helpful), we discussed how to structure the relationship between the microbiome…
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### Operating System
Windows 10
### Other Linux
_No response_
### Workflow Version
v2.10.1
### Workflow Execution
EPI2ME Desktop (Local)
### Other workflow execution
_No response_
### EPI2ME…
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based on some of the results for the new long-read benchmarking paper Portik et al. ([link](https://www.biorxiv.org/content/10.1101/2022.01.31.478527v1) - not yet updated), @bluegenes and I were discu…
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Hi all,
We are trying to get this pipeline working with the included control dataset so we can use it to characterize a variety of novel bacteriophages that we think may be circularly permuted with…
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I have noticed that the chloroplast and mitochondrion do not assemble with hifiasm. I am not expecting to get the full plastid assembled correctly, but I don't see anything. When I align the corrected…
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Ref #606.
The reviewers for [Pierce et al., 2019](https://f1000research.com/articles/8-1006) were enthusiastic about some of the algorithmic ideas we hinted at in sourmash (and correctly pointed ou…
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A good starting point is Pfam_SARS. I reviewed it a few weeks ago, and IIRC it has pretty good coverage of Betacov genes, but doesn't include some of the genes towards the 3' end found in other genera…