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Load in store app.
Sync to datacollector app.
OrganismNameOriginal
Abiotrophia defectiva
Achromobacter (alcaligenes) xylosoxidans
Achromobacter anxifer
Achromobacter denitrificans
Achromobact…
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Dear Iqbal lab,
I have sequences from an MTB isolate which is a known 50:50 mixture between two different strains, one of which is RIF resistant due to the H455Y mutation in the rpoB gene. In the J…
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When checking species specificity, samples can be discarded because Kraken may classify reads as Mycobacterium, rather than Mycobacterium tuberculosis. However, the code (below) only checks for Mycoba…
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Example:
```
ncbi = NCBITaxa()
descendants = ncbi.get_descendant_taxa(1763) # taxid of Mycobacterium
```
77643, taxid for Mycobacterium tuberculosis complex (species group) is not in descenda…
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Fatal error: Exit code 1 ()
2018-04-30 17:39:08,306 DEBUG: Namespace(files=[], force=False, input_directory=None, input_fasta_genome_name=None, json=False, keep_tmp=False, low_cov_depth_freq=20, low_…
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Hi,
What is the difference between R vs r in the resistance report?
For example see Quinolones in the report below: Thanks.
Probe sets :tb-species-170421.fasta.gz,tb-walker…
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See https://gist.github.com/ctb/9deb40a68108256ab4fd84c6b8e92e01 for implementation.
cc @brooksph @taylorreiter
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Dear Peter,
I feel so lucky to find such a scirpt you wrote to solve the taxid problem from diamond output. However, when I run Diamond_blast_to_taxid.py, I got a problem like this:
**Traceback (m…
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Hi there,
The pipeline seem to run fine until I reach step 11:
Here is the error from the meta_paths_run_log.txt
![screen shot 2014-02-25 at 3 23 21 pm](https://f.cloud.github.com/assets/6787918/2264…
maepz updated
7 years ago
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I am following the directions from https://github.com/katholt/srst2#using-the-vfbd-virulence-factor-database-with-srst2 to generate a VFDB gene database for Mycobacterium. I have already run these com…