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**Is your request related to a specific disease? Please describe.**
'common cold' (DOID:10459) and 'scarlet fever' (DOID:8596) are not properly classified in the infectious disease branch (should be …
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We use Kraken (now kraken2) for a lot of our analysis, and it would be great if there was a way to read kraken2 data in to kronatools. There probably is a way to do it using ktImportText, but I can't …
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Dear INNUCA team,
Is it possible to run INNUCA for other species than the one listed in the below modules?
https://github.com/B-UMMI/INNUca/tree/master/modules/trueCoverage_rematch
[campylobact…
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Extrapolated from common sequencing targets from the SRA, and sequences that returned false positives during initial database screenings:
- Human genome - integration sites: https://hgdownload.soe.…
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I download MLST database by `download_mlst_databases` and make `export MLST_DATABASES=/export/data/user/MLSTdb`
```
(base) [user@bigmem01 STRP-2020]$ get_sequence_type -a
Achromobacter spp
Acineto…
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I was reviewing the MaltExtract outputs and noticed that results for specific organisms (listed below) are missing:
- Achromobacter denitrificans
- Bacteroides vulgatus
- Citrobacter koseri
- En…
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Hello, I am running AMRFinderPlus on a large dataset that includes some _Burkholderia mallei_ samples. I specified `--organism Burkholderia_mallei` for these samples, assuming the supported species we…
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@TwistedSwisster kindly passed on the original reports from COADD that he and @AlvaroLor used to form the origin of this series. I've uploaded them [here](https://github.com/opensourceantibiotics/Seri…
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I was trying to test CRIPRSdisco on known data from crisprdb ["Streptococcus pyogenes A20"](https://crispr.i2bc.paris-saclay.fr/crispr/crispr_db.php?checked%5B%5D=NC_018936)
So I've downloaded NC_018…
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Add profile for basic analysis of Streptococcus pyogenes.
This is is of lower prio than the other organisms in #291, #302 & #303, but still something that has been asked for.