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Hi authors,
I have paired end fastq files of cell free DNA patients infected with sepsis. I have 6 patients files
For these 6 patients the distribution is as follows
Patient 1:
Leuconost…
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Streptococcus pneumoniae (pneumococcal disease)
https://www.cdc.gov/pneumococcal/clinicians/streptococcus-pneumoniae.html
https://www.ncbi.nlm.nih.gov/books/NBK470537/
https://www.who.int/teams/health…
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ch.fhir.ig.ch-vacd#5.0.0-ballot /artifacts.html
1252708008
Vaccine product containing only Streptococcus pneumoniae Danish serotype 1, 3, 4, 5, 6A, 6B, 7F, 9V, 14, 18C, 19A, 19F, 22F, 23F, and 33F ca…
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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 have tried the bcftools csq command with the attached fasta, and three different gff files (one from ncbi, one ncbi modified to add transcripts, and one from ensembl bacteria). In all cases the gff …
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Some genomes downloaded from PATRIC had genes with incorrect genome coordinates. For example, gene id 1313.4609.peg.100 from genome id 1313.4609 from species id Streptococcus_pneumoniae_58285.
This…
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- [x] Neisseria gonorrhea
- [x] Bordetella hinzi
- [x] Bordetella avium
- [x] Mycobacterium tuberculosis
- [x] Salmonella Typhi
- [x] Mycoplasma genitalium
- [x] Pseudomonas aeruginosa
- [x] Ra…
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Would you mind posting the mapping files? :)
![bitmoji](https://sdk.bitmoji.com/render/panel/c1ce9c0a-a16e-4d00-a3e1-049b89d14f03-50226b07-8b48-4219-bd53-027ed9816db2-v1.png?transparent=1&palette=…
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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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### Context
Unable to create new bacteria transcriptome indices after merging in new mappings via https://github.com/AlexsLemonade/refinebio/pull/3366.
In order to create a new transcriptome ind…