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**Describe the bug**
Downloading genome information on the Assembly BioSample Strain yields a column name containing an extra whitespace
**To Reproduce**
`datasets summary genome accession GCF_00…
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Current default configs for `strain` requires it to be a non-empty string with `accession` as the backup field.
https://github.com/nextstrain/pathogen-repo-guide/blob/89b3c5dbc9b8f6a009f4a19c3ac561…
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abbreviation limited to 5 characters, not handled. nothing to say we cant enter more than 5. we can enter empty fields by hitting space bar. nothing to say how many characters we can enter for each f…
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Dear authors,
I have been working on reproducing the results from your paper using the last.ckpt but have noticed some differences between the results I obtained and those reported in the paper.…
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### -> submitter ORCID (or name)
Finch, Melanie
### -> slug
finch-2024-cprime
### -> license
CC-BY-4.0
### -> alternative license URL
_No response_
### -> model category
model published in st…
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As discussed in #85, we need a way to warn users if their sample likely contains multiple strains. For now, we decided that we would like to add a warning based on CheckM2 statistics.
Basic idea:
…
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Hi,
I want to analyze my test piece VSG strain, but is the DICe gauge size which is equal to the strain window (window size)?
I have seen the video (DICe Demo 2D), and Speaker said that gauge size …
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In R script makeSeqsFiles.r I use part of a gene name before five digits as a strain name. It`s ok for prokka, but not a general solution.
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Hallo,
I have some questions about the use of Phylophlan as phylogenetic analysis for microbial isolates/genomes :
- Is it correct to use Phylophlan for detecting persistent strains ?
- How d…