Mercurial > repos > iuc > tbprofiler

view test-data/results_2.txt @ 17:d03af1c7002c draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 361de6d5f86e66c5ce996cdb37998408b3c28ae5
author iuc
date Mon, 11 Mar 2024 21:48:49 +0000
parents 8529c9fd63ad
children
line wrap: on
line source


TBProfiler report
=================

The following report has been generated by TBProfiler.

Summary
-------
ID: tbprofiler
Date: Mon Apr  1 10:38:29 2019
Strain: lineage2.2.2
Drug-resistance: Drug-resistant

Lineage report
--------------
Lineage	Estimated Fraction	Family	Spoligotype	Rd
lineage2	1.000	East-Asian	Beijing	RD105
lineage2.2	1.000	East-Asian (Beijing)	Beijing-RD207	RD105;RD207
lineage2.2.2	1.000	East-Asian (Beijing)	Beijing-RD105/RD207	RD105;RD207


Resistance report
-----------------
Drug	Genotypic Resistance	Mutations
ethionamide		
levofloxacin		
ofloxacin		
pyrazinamide		
amikacin		
delamanid		
cycloserine		
rifampicin	R	rpoB p.Asp435Val (1.00)
fluoroquinolones		
para-aminosalicylic acid		
capreomycin		
moxifloxacin		
ciprofloxacin		
ethambutol		
isoniazid		
aminoglycosides		
streptomycin		
linezolid		
kanamycin		
bedaquiline		
clofazimine		


Other variants report
---------------------
Genome Position	Locus Tag	Change	Estimated Fraction
763031	Rv0667	c.3225T>C	1.000
1834177	Rv1630	c.636A>C	1.000


Analysis pipeline specifications
--------------------------------
Version: 2.1.1
Analysis	Program
Mapping	bwa
Variant Calling	BCFtools


Disclaimer
----------
This tool is for Research Use Only and is offered free foruse. The London School
of Hygiene and Tropical Medicine shall have no liability for any loss or damages
of any kind, however sustained relating to the use of this tool.

Citation
--------
Coll, F. et al. Rapid determination of anti-tuberculosis drug resistance from
whole-genome sequences. Genome Medicine 7, 51. 2015