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Beyond the Command-
    Line Interface:
Transcriptome Analysis based on Next-Generation-
                Sequencing Data
Beyond the Command-
    Line Interface:
Transcriptome Analysis based on Next-Generation-
                Sequencing Data
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation




                 Transcriptome Analysis

                 • cheap to produce
                 • fast way of producing data
                 • allows comparative analysis
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation




                                               Assembly
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation




                                               Assembly
                                                                            read
                                                                                 III
                                         read 1


                                              1V                                read 1I
                                        re ad
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation




                                               Assembly


                                         read 1I                    read 1V


                                          read 1                     read III
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation




                                               Assembly
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation




                                               Assembly
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation




                                          Annotation




                                                                   Image: http://commons.wikimedia.org/wiki/User:Rama, CC-BY-SA 2.0
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation




                                          Annotation




                                                                   Image: http://commons.wikimedia.org/wiki/User:Rama, CC-BY-SA 2.0
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Assembly / Annotation




                                          Annotation




                                                                   Image: http://commons.wikimedia.org/wiki/User:Rama, CC-BY-SA 2.0
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Tools / Interfaces / Drawbacks




                    What tools do exist?
                     How is it done?
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Tools / Interfaces / Drawbacks




                                 How is it done?


                    What tools do exist?
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Tools / Interfaces / Drawbacks




                    What tools do exist?
                     How is it done?
                                                   SNP-               Homology-         ORF-
                           Assembly
                                                 Detection            Detection       Prediciton


                                 CAP3            QualitySNP                BLAST        ESTScan



                                 MIRA              AutoSNP            FASTX/FASTY     ORFPredictor



                                                   PolyBayes              HMMER



                                                     MIRA             PatternHunter
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Tools / Interfaces / Drawbacks
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Tools / Interfaces / Drawbacks




                                                                                            word count
                                                                                  Tool
                                                                                           of the manual



                                                                                BLAST2GO        618



                                                                                 BLAST         3469



                                                                                 HMMER         32213



                                                                                  MIRA         71654
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Tools / Interfaces / Drawbacks




                                           Drawbacks

                 • spoilt for choice by the amount of tools
                 • time-consuming to find right tools
                 • lots of parameters to learn
                 • the command-line interface is unintuitive

                                                                                Chin et al, 1998
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby




                                 Beyond the CLI
                                       Getting around the Drawbacks



              • minimize choice of tools
              • minimize the parameters for each tool
              • add a graphical user interface


                                                                                Chin et al, 1998
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby



                                                  Pipeline
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby



                                                  Pipeline
                                                                                    Task              Tool

                                                                                                  Perl- & Python-
                                                                                File-Conversion
                                                                                                       Scripts

                                                                                   Assembly           MIRA

                                                                                SNP-Detection         MIRA

                                                                                  Homology-
                                                                                                      BLAST
                                                                                  Detection

                                                                                ORF-Prediction    ORFPredictor

                                                                                                   pfam_scan /
                                                                                Pfam-Annotation
                                                                                                     HMMER

                                                                                GO-Annotation      BLAST2GO
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby



                                                  Pipeline
                                                                                    Task              Tool

                                                                                                  Perl- & Python-
                                                                                File-Conversion
                                                                                                       Scripts

                                                                                   Assembly           MIRA

                                                                                SNP-Detection         MIRA

                                                                                  Homology-
                                                                                                      BLAST
                                                                                  Detection

                                                                                ORF-Prediction    ORFPredictor

                                                                                                   pfam_scan /
                                                                                Pfam-Annotation
                                                                                                     HMMER

                                                                                GO-Annotation      BLAST2GO
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby



                                                  Pipeline
                                                                                    Task              Tool

                                                                                                  Perl- & Python-
                                                                                File-Conversion
                                                                                                       Scripts

                                                                                   Assembly           MIRA

                                                                                SNP-Detection         MIRA

                                                                                  Homology-
                                                                                                      BLAST
                                                                                  Detection

                                                                                ORF-Prediction    ORFPredictor

                                                                                                   pfam_scan /
                                                                                Pfam-Annotation
                                                                                                     HMMER

                                                                                GO-Annotation      BLAST2GO
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby



                                                  Pipeline
                                                                                    Task              Tool

                                                                                                  Perl- & Python-
                                                                                File-Conversion
                                                                                                       Scripts

                                                                                   Assembly           MIRA

                                                                                SNP-Detection         MIRA

                                                                                  Homology-
                                                                                                      BLAST
                                                                                  Detection

                                                                                ORF-Prediction    ORFPredictor

                                                                                                   pfam_scan /
                                                                                Pfam-Annotation
                                                                                                     HMMER

                                                                                GO-Annotation      BLAST2GO
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby




                                                           GUI
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby




                                                           GUI
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby




                                                           GUI
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby




                                                           GUI
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby




                                                           GUI
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby




                                                           GUI
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby




                                                           GUI
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby




                                                           GUI
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby




                                                           GUI
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby




                                                           GUI
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby




                              Distributed Ruby
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Solutions / Pipeline / GUI / Distributed Ruby




                              Distributed Ruby
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Zostera marina / Results



                                                    Results


                                                                                Zostera marina




                                                                                   Image: Colin Faulkingham, CC-BY-SA 2.5
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Zostera marina / Results



                                                    Results


                                                                                Zostera marina
                                                                                866838 454-reads




                                                                                    Image: Colin Faulkingham, CC-BY-SA 2.5
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Zostera marina / Results



                                                    Results


                                                                                Zostera marina
                                                                                866838 454-reads


                                                                                 35364 contigs



                                                                                    Image: Colin Faulkingham, CC-BY-SA 2.5
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Zostera marina / Results
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Zostera marina / Results
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Zostera marina / Results
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Zostera marina / Results
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Shortcomings & Solutions / Summary



                                     Shortcomings

                 • only basic analysis due to lack of
                       parameters of single tools
                 • no graphical representation of results
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Shortcomings & Solutions / Summary



                                     Shortcomings
                 • only basic analysis due to lack of
                       parameters of single tools
                 • no graphical representation of results
                                                  Solutions
                • add optional “expert” parameters
                • implement graphical representations
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Shortcomings & Solutions / Summary




                                               Summary

                 • Transcriptome Analysis needs software
                       tools
                 • Many different tools for each task exist
                 • Most of them are CLI-driven
                 • People don‘t like the CLI
Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook
Shortcomings & Solutions / Summary




                                               Summary
                 • Built a pipeline that provides usual tools
                       and a GUI
                 • The pipeline works for standard tasks of
                       Transcriptome Analysis
                 • In an upcoming version more tool-
                       parameters & graphical results shall be
                       added
it´s your turn: feel free
    to ask questions




              image: Joe Rosenthal & Shigeru Miyamoto (fair use)
it´s your turn: feel free
    to ask questions




              image: Joe Rosenthal & Shigeru Miyamoto (fair use)

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Defense of my BSc-Thesis

  • 1. Beyond the Command- Line Interface: Transcriptome Analysis based on Next-Generation- Sequencing Data
  • 2. Beyond the Command- Line Interface: Transcriptome Analysis based on Next-Generation- Sequencing Data
  • 3. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Assembly / Annotation Transcriptome Analysis • cheap to produce • fast way of producing data • allows comparative analysis
  • 4. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Assembly / Annotation Assembly
  • 5. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Assembly / Annotation Assembly read III read 1 1V read 1I re ad
  • 6. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Assembly / Annotation Assembly read 1I read 1V read 1 read III
  • 7. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Assembly / Annotation Assembly
  • 8. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Assembly / Annotation Assembly
  • 9. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Assembly / Annotation Annotation Image: http://commons.wikimedia.org/wiki/User:Rama, CC-BY-SA 2.0
  • 10. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Assembly / Annotation Annotation Image: http://commons.wikimedia.org/wiki/User:Rama, CC-BY-SA 2.0
  • 11. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Assembly / Annotation Annotation Image: http://commons.wikimedia.org/wiki/User:Rama, CC-BY-SA 2.0
  • 12. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Tools / Interfaces / Drawbacks What tools do exist? How is it done?
  • 13. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Tools / Interfaces / Drawbacks How is it done? What tools do exist?
  • 14. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Tools / Interfaces / Drawbacks What tools do exist? How is it done? SNP- Homology- ORF- Assembly Detection Detection Prediciton CAP3 QualitySNP BLAST ESTScan MIRA AutoSNP FASTX/FASTY ORFPredictor PolyBayes HMMER MIRA PatternHunter
  • 15. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Tools / Interfaces / Drawbacks
  • 16. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Tools / Interfaces / Drawbacks word count Tool of the manual BLAST2GO 618 BLAST 3469 HMMER 32213 MIRA 71654
  • 17. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Tools / Interfaces / Drawbacks Drawbacks • spoilt for choice by the amount of tools • time-consuming to find right tools • lots of parameters to learn • the command-line interface is unintuitive Chin et al, 1998
  • 18. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby Beyond the CLI Getting around the Drawbacks • minimize choice of tools • minimize the parameters for each tool • add a graphical user interface Chin et al, 1998
  • 19. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby Pipeline
  • 20. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby Pipeline Task Tool Perl- & Python- File-Conversion Scripts Assembly MIRA SNP-Detection MIRA Homology- BLAST Detection ORF-Prediction ORFPredictor pfam_scan / Pfam-Annotation HMMER GO-Annotation BLAST2GO
  • 21. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby Pipeline Task Tool Perl- & Python- File-Conversion Scripts Assembly MIRA SNP-Detection MIRA Homology- BLAST Detection ORF-Prediction ORFPredictor pfam_scan / Pfam-Annotation HMMER GO-Annotation BLAST2GO
  • 22. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby Pipeline Task Tool Perl- & Python- File-Conversion Scripts Assembly MIRA SNP-Detection MIRA Homology- BLAST Detection ORF-Prediction ORFPredictor pfam_scan / Pfam-Annotation HMMER GO-Annotation BLAST2GO
  • 23. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby Pipeline Task Tool Perl- & Python- File-Conversion Scripts Assembly MIRA SNP-Detection MIRA Homology- BLAST Detection ORF-Prediction ORFPredictor pfam_scan / Pfam-Annotation HMMER GO-Annotation BLAST2GO
  • 24. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby GUI
  • 25. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby GUI
  • 26. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby GUI
  • 27. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby GUI
  • 28. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby GUI
  • 29. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby GUI
  • 30. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby GUI
  • 31. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby GUI
  • 32. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby GUI
  • 33. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby GUI
  • 34. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby Distributed Ruby
  • 35. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Solutions / Pipeline / GUI / Distributed Ruby Distributed Ruby
  • 36. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Zostera marina / Results Results Zostera marina Image: Colin Faulkingham, CC-BY-SA 2.5
  • 37. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Zostera marina / Results Results Zostera marina 866838 454-reads Image: Colin Faulkingham, CC-BY-SA 2.5
  • 38. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Zostera marina / Results Results Zostera marina 866838 454-reads 35364 contigs Image: Colin Faulkingham, CC-BY-SA 2.5
  • 39. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Zostera marina / Results
  • 40. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Zostera marina / Results
  • 41. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Zostera marina / Results
  • 42. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Zostera marina / Results
  • 43. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Shortcomings & Solutions / Summary Shortcomings • only basic analysis due to lack of parameters of single tools • no graphical representation of results
  • 44. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Shortcomings & Solutions / Summary Shortcomings • only basic analysis due to lack of parameters of single tools • no graphical representation of results Solutions • add optional “expert” parameters • implement graphical representations
  • 45. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Shortcomings & Solutions / Summary Summary • Transcriptome Analysis needs software tools • Many different tools for each task exist • Most of them are CLI-driven • People don‘t like the CLI
  • 46. Transcriptome Analysis / How is it done? / Beyond the CLI / Results / Outlook Shortcomings & Solutions / Summary Summary • Built a pipeline that provides usual tools and a GUI • The pipeline works for standard tasks of Transcriptome Analysis • In an upcoming version more tool- parameters & graphical results shall be added
  • 47. it´s your turn: feel free to ask questions image: Joe Rosenthal & Shigeru Miyamoto (fair use)
  • 48. it´s your turn: feel free to ask questions image: Joe Rosenthal & Shigeru Miyamoto (fair use)