Mercurial > repos > iuc > tbprofiler

annotate test-data/results_2.txt @ 3:19793eecc9f0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 5679ad1f1d5cac6c6168ad91dd4ca3616d22ca35"
author iuc
date Fri, 16 Aug 2019 16:26:31 -0400
parents 8529c9fd63ad
children
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8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
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1
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
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2 TBProfiler report
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3 =================
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4
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5 The following report has been generated by TBProfiler.
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6
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
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7 Summary
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8 -------
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
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9 ID: tbprofiler
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10 Date: Mon Apr 1 10:38:29 2019
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11 Strain: lineage2.2.2
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12 Drug-resistance: Drug-resistant
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13
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
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14 Lineage report
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15 --------------
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
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16 Lineage Estimated Fraction Family Spoligotype Rd
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17 lineage2 1.000 East-Asian Beijing RD105
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18 lineage2.2 1.000 East-Asian (Beijing) Beijing-RD207 RD105;RD207
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
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19 lineage2.2.2 1.000 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
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21
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22 Resistance report
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23 -----------------
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24 Drug Genotypic Resistance Mutations
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25 ethionamide
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26 levofloxacin
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27 ofloxacin
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28 pyrazinamide
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29 amikacin
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30 delamanid
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31 cycloserine
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32 rifampicin R rpoB p.Asp435Val (1.00)
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
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33 fluoroquinolones
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34 para-aminosalicylic acid
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35 capreomycin
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36 moxifloxacin
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37 ciprofloxacin
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38 ethambutol
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39 isoniazid
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40 aminoglycosides
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41 streptomycin
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42 linezolid
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43 kanamycin
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44 bedaquiline
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45 clofazimine
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48 Other variants report
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49 ---------------------
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50 Genome Position Locus Tag Change Estimated Fraction
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51 763031 Rv0667 c.3225T>C 1.000
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52 1834177 Rv1630 c.636A>C 1.000
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53
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54
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55 Analysis pipeline specifications
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56 --------------------------------
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57 Version: 2.1.1
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58 Analysis Program
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59 Mapping bwa
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60 Variant Calling BCFtools
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61
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62
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63 Disclaimer
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64 ----------
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65 This tool is for Research Use Only and is offered free foruse. The London School
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66 of Hygiene and Tropical Medicine shall have no liability for any loss or damages
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67 of any kind, however sustained relating to the use of this tool.
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68
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69 Citation
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70 --------
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71 Coll, F. et al. Rapid determination of anti-tuberculosis drug resistance from
8529c9fd63ad planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit ef7cfd0c271f1ec40d3df3be4c91bb71028e85e8
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72 whole-genome sequences. Genome Medicine 7, 51. 2015