Mercurial > repos > iuc > tbprofiler
comparison test-data/results_2.txt @ 0:8529c9fd63ad draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
| author | iuc |
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| date | Tue, 02 Apr 2019 09:03:16 -0400 |
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| -1:000000000000 | 0:8529c9fd63ad |
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| 1 | |
| 2 TBProfiler report | |
| 3 ================= | |
| 4 | |
| 5 The following report has been generated by TBProfiler. | |
| 6 | |
| 7 Summary | |
| 8 ------- | |
| 9 ID: tbprofiler | |
| 10 Date: Mon Apr 1 10:38:29 2019 | |
| 11 Strain: lineage2.2.2 | |
| 12 Drug-resistance: Drug-resistant | |
| 13 | |
| 14 Lineage report | |
| 15 -------------- | |
| 16 Lineage Estimated Fraction Family Spoligotype Rd | |
| 17 lineage2 1.000 East-Asian Beijing RD105 | |
| 18 lineage2.2 1.000 East-Asian (Beijing) Beijing-RD207 RD105;RD207 | |
| 19 lineage2.2.2 1.000 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 | |
| 20 | |
| 21 | |
| 22 Resistance report | |
| 23 ----------------- | |
| 24 Drug Genotypic Resistance Mutations | |
| 25 ethionamide | |
| 26 levofloxacin | |
| 27 ofloxacin | |
| 28 pyrazinamide | |
| 29 amikacin | |
| 30 delamanid | |
| 31 cycloserine | |
| 32 rifampicin R rpoB p.Asp435Val (1.00) | |
| 33 fluoroquinolones | |
| 34 para-aminosalicylic acid | |
| 35 capreomycin | |
| 36 moxifloxacin | |
| 37 ciprofloxacin | |
| 38 ethambutol | |
| 39 isoniazid | |
| 40 aminoglycosides | |
| 41 streptomycin | |
| 42 linezolid | |
| 43 kanamycin | |
| 44 bedaquiline | |
| 45 clofazimine | |
| 46 | |
| 47 | |
| 48 Other variants report | |
| 49 --------------------- | |
| 50 Genome Position Locus Tag Change Estimated Fraction | |
| 51 763031 Rv0667 c.3225T>C 1.000 | |
| 52 1834177 Rv1630 c.636A>C 1.000 | |
| 53 | |
| 54 | |
| 55 Analysis pipeline specifications | |
| 56 -------------------------------- | |
| 57 Version: 2.1.1 | |
| 58 Analysis Program | |
| 59 Mapping bwa | |
| 60 Variant Calling BCFtools | |
| 61 | |
| 62 | |
| 63 Disclaimer | |
| 64 ---------- | |
| 65 This tool is for Research Use Only and is offered free foruse. The London School | |
| 66 of Hygiene and Tropical Medicine shall have no liability for any loss or damages | |
| 67 of any kind, however sustained relating to the use of this tool. | |
| 68 | |
| 69 Citation | |
| 70 -------- | |
| 71 Coll, F. et al. Rapid determination of anti-tuberculosis drug resistance from | |
| 72 whole-genome sequences. Genome Medicine 7, 51. 2015 |