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Coding & Best Practice in Programming in the NGS era
- 1. Coding & Best Practice in Programming Why it matters so much in the NGS era Lex Nederbragt Norwegian Sequencing Centre and Centre for Evolutionary and Ecological Synthesis lex.nederbragt@ibv.uio.no @lexnederbragt OK
- 2. Who am I @lexnederbragt flxlexblog.wordpress.com
- 3. How I became a bioinformatician
- 4. 2007: a grant GS FLX from Roche/454 Genome Analyzer from Solexa/Illumina ? Let’s try them out!
- 5. Specimen • Planktothrix rubescens NIVA CYA 98 • Cyanobacteria • (blue-green algae)
- 6. Planktothrix Half a million reads Average length 260 nt 10 million reads 33 nucleotides each Perl
- 7. Planktothrix Newbler SHARCGS Assembly Half a million reads Average length 260 nt 10 million reads 33 nucleotides each
- 8. Atlantic cod genome project 850 million bases (Mbp )‘Wild-caught’ GS FLX from Roche/454
- 9. Atlantic cod genome project phase 1
- 10. Cod genome project phase 2 From Wikimedia commons, user Sagar Joshi
- 11. In summary From flickr, user lesterpubliclibrary
- 12. Challenges in the next-generation sequencing era
- 13. High-throughput sequencing Phase 1: more is better Phase 2: smaller is better Phase 3: single-molecule Phase 4: nanopores
- 14. Democratization of sequencing MinION 512 nanopores 150mb/hour Up to 6 hours $900
- 15. Sequencing cost Thanks to Matt Clark (TGAC), modified from http://bit.ly/1iiajcS 454 & polony Solexa & SOLiD HiSeq HiSeq X Ten GAII End of the gold rush?
- 16. More more more Data Software Mathias Bigge, Ricordisamoa, others (wikimedia commons) TCTCCTAACAACCCCCcACACACACACACTGGTA CTGATGCCATTCTGCTTTACACCTATACACATCA TATACATtATACACACACACACACACACACAACA CTCTCCTAACCCACACACACTGGTACAGATGCCA GTCTGCTTAACACCTACGCACGTATTATACACAC ACACACACAACGCTCTCCTAACCCACACACACAC CAGTCTGCTTTAAACCTACACACATATTATACAA ACGAGTTGGTGACGTAAGGTTGATAAGGGATATT GGTAAGGGTTAAGGGTAGGGTTGGTGTTAGGGGC AAGGGTTAGGGTTAGTGTAAGGGGTAAGGGTTAG TGTAaGGAGTAAGGGTTAGTGTAAGGGGTTAGTG TTATTGTAAGGGGCTAGTGTTAGTGTTAGTGTTC AGGGTTAGTGTTAGGGGTAGGGTTAATgTTTAGG GTAATGTTTAGGGTTAGGGGTATGGGTTAGTGCT AGGGGTCAGGGTTAGTGTTAGGGTTAGACAACCC ACCTGAGAGAACCAGTGCGATGCCGCCGCAGGCG TTGGGCGAGGACATGGAGGTGCCGTTCATCAGCT GGGTCCCCCGGAGGGTCCAGTTGGGGACGGAGGC GATGGCTCCCCCCGGAGCGCTGATGCTGACCCCC AGGGCGCCGTCGATGCTGGGTCCCCGAGACGACC AGGTGTACTGGTTGGCCGGGAGCTTCTCCCTCAG GGAGTACTCCGCCACCATCATGTCGGGGGTCACG TAGGCCCCAACCCCTGGGGACAGACGGAGCGCGT TACACACCTCAACCCCTTACCCTCGGAGCCTACA
- 17. Software Constant stream of new software http://wwwdev.ebi.ac.uk/fg/hts_mappers 88 short-read mappers
- 18. Software Constant stream of new software http://neidetcher.com/ubuntu_package_dependency.html InstallationJudging quality Wikimedia commons, user Thebestofall007
- 19. Do we need to be worried?
- 20. Do we need to be worried? Self-taught bioinformaticians ACCCCCcACACACACACACTGGTACTGATGCC ACACCTATACACATCATATACATtATACACAC ACACAACACTCTCCTAACCCACACACACTGGT GTCTGCTTAACACCTACGCACGTATTATACAC AACGCTCTCCTAACCCACACACACACCAGTCT TACACACATATTATACAAACGAGTTGGTGACG AAGGGATATTGGTAAGGGTTAAGGGTAGGGTT GCAAGGGTTAGGGTTAGTGTAAGGGGTAAGGG GAGTAAGGGTTAGTGTAAGGGGTTAGTGTTAT TAGTGTTAGTGTTAGTGTTCAGGGTTAGTGTT TTAATgTTTAGGGTAATGTTTAGGGTTAGGGG TGCTAGGGGTCAGGGTTAGTGTTAGGGTTAGA GAGAGAACCAGTGCGATGCCGCCGCAGGCGTT ATGGAGGTGCCGTTCATCAGCTGGGTCCCCCG TTGGGGACGGAGGCGATGGCTCCCCCCGGAGC ACCCCCAGGGCGCCGTCGATGCTGGGTCCCCG GTGTACTGGTTGGCCGGGAGCTTCTCCCTCAG GCCACCATCATGTCGGGGGTCACGTAGGCCCC GACAGACGGAGCGCGTTACACACCTCAACCCC AGCCTACATAACCCAACCCTCTGGAGACGGCA AGTCAGAAATAGaGCTGACCGATTCATCAAAT lot’s of data lot’s of software recipe for disaster?
- 24. What it boils down to
- 25. My (given) title Coding & Best Practice in Programming Why it matters so much in the NGS era Why it matters so much in science Next-generation sequencing specific?
- 26. Diagnostic sequencing Wikimedia commons, user Bill Branson
- 29. Solutions
- 30. Solutions Flickr: http://farm4.staticflickr.com/3319/3265787219_bfbc654b5e_o.jpg Wikimedia commons
- 32. Best practices Automate repetitive tasks Wikimedia commons, user Pzucchel
- 33. Best practices Coding styles, variable naming etc def test_seq: def sequence_is_DNA:
- 34. Best practices Use version control https://www.atlassian.com/git/workflows
- 35. Best practices From my own work: $ cd scripts $ ls blat_parse4.pl old_versions snps_flanks_2_fastq.pl $ ls old_versions/ blat_parse2.pl blat_parse_attemp1.pl blat_parse.pl.bak blat_parse.pl blat_parse3_backup.pl blat_parse3.pl
- 36. Best practices test, test, test def test_zero: assert run_the_function(0) == 0 Assert x > 0, ”cannot handle negative numbers"
- 38. Best practices Collaborate http://howdoitradestocks.com/wp-content/uploads/2011/12/share-ideas1.jpg
- 39. khmer, a 'case study'
- 40. khmer Crusoe et al. doi: 10.6084/m9.figshare.979190Michael Crusoe Titus Brown
- 42. khmer Integrated code coverage analysis The “GitHub Flow” model of code review Semantic versioning Continuous integrationIntegration and acceptance testing
- 43. Beyond best coding practices
- 46. Benchmarks http://www.genomeinabottle.org/ ~8300 10ug vials of DNA for NA12878
- 50. Action points
- 51. Action points Attend a software Carpentry Boot Camp http://software-carpentry.org/
- 52. Action points Look for signs of best practice
- 53. Action points Look for signs of best practice during peer review nature.com
- 55. Action points Develop (under)graduate curriculum
- 56. My goal today Flickr: http://farm4.staticflickr.com/3319/3265787219_bfbc654b5e_o.jpg
Notes de l'éditeur
- pre-merge code reviews.pair programming issue tracking
- develop the reference materials, reference data, and reference methods needed to assess performance of human genome sequencing.