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Coding & Best Practice in Programming in the NGS era
- 1. Coding & BestPractice 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 @lexnederbragtflxlexblog.wordpress.com
- 3. How I becamea bioinformatician
- 4. 2007: a grant GSFLX from Roche/454 Genome Analyzer from Solexa/Illumina ? Let’s try them out!
- 5. Specimen • Planktothrix rubescensNIVA CYA 98 • Cyanobacteria • (blue-green algae)
- 6. Planktothrix Half a millionreads Average length 260 nt 10 million reads 33 nucleotides each Perl
- 7. Planktothrix Newbler SHARCGS Assembly Half amillion reads Average length 260 nt 10 million reads 33 nucleotides each
- 8. Atlantic cod genomeproject 850 million bases (Mbp )‘Wild-caught’ GS FLX from Roche/454
- 9. Atlantic cod genomeproject phase 1
- 10. Cod genome projectphase 2 From Wikimedia commons, user Sagar Joshi
- 11. In summary From flickr,user lesterpubliclibrary
- 12. Challenges in thenext-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 512nanopores 150mb/hour Up to 6 hours $900
- 15. Sequencing cost Thanks toMatt 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 DataSoftware 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 ofnew software http://wwwdev.ebi.ac.uk/fg/hts_mappers 88 short-read mappers
- 18. Software Constant stream ofnew software http://neidetcher.com/ubuntu_package_dependency.html InstallationJudging quality Wikimedia commons, user Thebestofall007
- 19. Do we needto be worried?
- 20. Do we needto 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?
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- 24. What it boilsdown 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
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- 32. Best practices Automate repetitivetasks Wikimedia commons, user Pzucchel
- 33. Best practices Coding styles,variable naming etc def test_seq: def sequence_is_DNA:
- 34. Best practices Use versioncontrol https://www.atlassian.com/git/workflows
- 35. Best practices From myown 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"
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- 39. khmer, a 'casestudy'
- 40. khmer Crusoe et al.doi: 10.6084/m9.figshare.979190Michael Crusoe Titus Brown
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- 42. khmer Integrated code coverage analysis The“GitHub Flow” model of code review Semantic versioning Continuous integrationIntegration and acceptance testing
- 43. Beyond best codingpractices
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- 46. Benchmarks http://www.genomeinabottle.org/ ~8300 10ug vialsof DNA for NA12878
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- 51. Action points Attend asoftware Carpentry Boot Camp http://software-carpentry.org/
- 52. Action points Look forsigns of best practice
- 53. Action points Look forsigns of best practice during peer review nature.com
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- 55. Action points Develop (under)graduatecurriculum
- 56. My goal today Flickr:http://farm4.staticflickr.com/3319/3265787219_bfbc654b5e_o.jpg