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Covstats can report that over 3000% of a sample is unmapped.
## Example
[BioSample SAMN18146202](https://www.ncbi.nlm.nih.gov/biosample/SAMN18146202/) is a simulated _Mycobacterium tuberculosis_ s…
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I tried running the following given the GCF file provided by NCBI and it didn’t work:
```
singularity exec --bind /data depot.galaxyproject.org-singularity-tb-profiler-6.2.0--pyhdfd78af_1.img tb-pro…
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Works "fine" on organism names made of 2 parts (this is the most common situation):
> BSgenomeForge:::abbreviate_organism_name("Homo sapiens")
[1] "Hsapiens"
> BSgenomeForge:::abbre…
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The `genus` and `species` fields can be checked against local `taxdump/genus.txt` and `taxdump/species.txt`.
(a) write generic TaxdumpLookup
(b) integrate it to `ami-phylo`
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Dear Mykrobe team,
according to your paper (Bradley et al. Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat Commun. 20…
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@lyonsm7: Do you know what the full names should be for each of the following columns in the summary datasheet?
- cLogP
- huPPB
- muPPB
- MIC_Erdman
- MICserumErd
- MIC_Rv
- Caseum_binding
…
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taobilin@VirtualBox:~$ tb-profiler update_tbdb
Running command:
set -u pipefail; git pull
Running command:
set -u pipefail; tb-profiler create_db
Traceback (most recent call last):
File "…
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I have a question regarding how tbprofiler assigns lineages. I understand that lineages are determined by identifying lineage-specific SNPs. However, I am not familiar with the specific details or alg…
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# tb-profiler error report
* OS: linux
* Program version: 4.4.2
* Database version: c2fb9a2
* Program call:
```
{'read1': '/etc/ace-data/home/sbabirye/data/fastq_Seq/ERR038736_LIB1_R1.fastq.gz…
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The following regular expression/s should allow (a) validation and (b) controlled correction of errors in the creation of tip labels in `ami-phylo`
```
…