Commits · 3370f1b8bdad80c8a1fad9500427f17a918ae806 · ESB / ONT_pilot_gitlab · GitLab

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Oct 07, 2020
- updated GDB config files (issue #54 ) · 3370f1b8
  Valentina Galata authored 4 years ago
  
  3370f1b8
- host contamination filtering w/ bbmap/bbtools (issue #54 ); other minor changes · 3abb643a
  Valentina Galata authored 4 years ago
  
  3abb643a
Sep 29, 2020
- added comment to diamond rule · d35ad664
  Valentina Galata authored 4 years ago
  
  d35ad664
Sep 22, 2020
- notes: script for segmentation analysis of contig cov (issue #84 ) · c2d4784c
  Valentina Galata authored 4 years ago
  
  c2d4784c
Sep 16, 2020
- report: updated plots (mostly themes) · c48ede7b
  Valentina Galata authored 4 years ago
  
  c48ede7b
Sep 15, 2020
- notes: plots and multimodality test for contig cov (issye #84 ) · b7870822
  Valentina Galata authored 4 years ago
  
  b7870822
- report: added shapes to cdhit scatter plot · d9e49f81
  Valentina Galata authored 4 years ago
  
  d9e49f81
Sep 14, 2020
- report: changed zoom in gene length plot · 53aba75b
  Valentina Galata authored 4 years ago
  
  53aba75b
- report: updated cdhit plots (issue #84 ) · 6a0c99c5
  Valentina Galata authored 4 years ago
  
  6a0c99c5
- report: minor change in report.R (axis titles in gene len fig) · b380f34c
  Valentina Galata authored 4 years ago
  
  b380f34c
- report: new cdhit summary and plots (issue #84 ); other minor changes · 9e197abd
  Valentina Galata authored 4 years ago
  
  9e197abd
- report: rm pack version from r.yaml (prev env version cannot be recreated) · aa32eadf
  Valentina Galata authored 4 years ago
  
  aa32eadf
- mapping/coverage: added utils/rule for ave gene/protein cov (issue #84 ) · 489c361b
  Valentina Galata authored 4 years ago
  
  489c361b
Sep 11, 2020
- mapping: changed genomecove_bg to per base coverage (issue #84 ) · e3af652b
  Valentina Galata authored 4 years ago
  
  e3af652b
- mapping: minor change in targets (ave cov for filtered contigs); new rule/targets (issue #84 ) · 7576bd59
  Valentina Galata authored 4 years ago
  
  7576bd59
Sep 10, 2020
- issue #77 : cov plot example - updated · 1600fdd4
  Valentina Galata authored 4 years ago
  
  1600fdd4
- issue #77 : cov plot example · 1257fcdb
  Valentina Galata authored 4 years ago
  
  1257fcdb
Sep 09, 2020
- Merge branch 'master' of ssh://git-r3lab-server.uni.lu:8022/susheel.busi/ont_pilot_gitlab · 66bfe0c3
  Valentina Galata authored 4 years ago
  
  66bfe0c3
- issue #77 : notes to collected and plot stats for specialtigs (cdhit results) · f49767ce
  Valentina Galata authored 4 years ago
  
  f49767ce
Aug 28, 2020
- Update Snakefile · 45fe154c
  Susheel Busi authored 4 years ago
  
  45fe154c
Aug 21, 2020
- report: minor updates for the plots · b783d5d6
  Valentina Galata authored 4 years ago
  
  b783d5d6
- report: fixed a bug in rule collecting cdhit results · b8aec505
  Valentina Galata authored 4 years ago
  
  b8aec505
- updated readme; configs: updated conda env path in all sbatch.sh files · cf5125be
  Valentina Galata authored 4 years ago
  
  cf5125be
- report: updated names/colors of assemblers in utils.R · d6aef8eb
  Valentina Galata authored 4 years ago
  
  d6aef8eb
- configs: sbatch.sh: run snakemake only if conda env activation has worked · 34ac0857
  Valentina Galata authored 4 years ago
  
  34ac0857
- notes: updated mashmap script · 1b257f12
  Valentina Galata authored 4 years ago
  
  1b257f12
- Update sbatch.sh · 38268814
  Susheel Busi authored 4 years ago
  
  38268814
Aug 20, 2020
- Zymo/GSI20 configs: replaced main conda env path · 4ac143ff
  Valentina Galata authored 4 years ago
  
  4ac143ff
- readme update · ea2bddb7
  Valentina Galata authored 4 years ago
  
  ea2bddb7
Aug 19, 2020
- notes: mashmap update · 04045c15
  Valentina Galata authored 4 years ago
  
  04045c15
- GIS20/Zymo configs: fixed a typo · 6fa78459
  Valentina Galata authored 4 years ago
  
  6fa78459
- notes: mashmap (issue #35 ) · 015d6d47
  Valentina Galata authored 4 years ago
  
  015d6d47
- updated configs · db86679c
  Valentina Galata authored 4 years ago
  
  db86679c
- polishing update: changed polishing strategy, updated racon conda yaml to... · 1ffcfe82
  Valentina Galata authored 4 years ago
  
  polishing update: changed polishing strategy, updated racon conda yaml to replace bwa conda yaml (issue #81)
  1ffcfe82
Aug 18, 2020
- notes: diamond test (issue #78 ) · dd75bd8f
  Valentina Galata authored 4 years ago
  
  dd75bd8f
- notes: infernal test · c2cd8ebc
  Valentina Galata authored 4 years ago
  
  c2cd8ebc
- report: numbers of cdhit stats (table) · 2659ef18
  Valentina Galata authored 4 years ago
  
  2659ef18
- better expression to list targets for assembly step · fef9a05c
  Valentina Galata authored 4 years ago
  
  fef9a05c
- updated GDB config: added mapping back to the steps · e71b9507
  Valentina Galata authored 4 years ago
  
  e71b9507
- report: update to include new assemblers; fixed tool order in cdhit/diamond plots · f45459a1
  Valentina Galata authored 4 years ago
  
  f45459a1