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?

21. Correctness of results
http://www.it.bton.ac.uk/staff/je/java/jewl/tutorial/tutorial.html

22. Reproducibility
doi:10.1038/sj.embor.7401143
A reproducibility crisis?

23. Reproducibility and reusability
http://upload.wikimedia.org/wikipedia/commons/4/48/Recycle.jpg

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

27. Diagnostic sequencing

28. Diagnostic sequencing

29. Solutions

30. Solutions
Flickr: http://farm4.staticflickr.com/3319/3265787219_bfbc654b5e_o.jpg Wikimedia commons

31. Best practices
10.1371/journal.pbio.1001745

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"

37. Best practices
Document well

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

41. khmer
https://github.com/ged-lab/2013-paper-ssspe

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

44. Benchmarks
http://assemblathon.org/

45. Benchmarks
http://www.genome.org/cgi/doi/10.1101/gr.131383.111

46. Benchmarks
http://www.genomeinabottle.org/
~8300 10ug vials of DNA for NA12878

47. (Assembly) validation

48. (Assembly) validation
Assembly
doi:10.1186/1471-2105-15-126

49. Reproducibility ‘platforms’
usegalaxy.org
taverna.org.uk/
pythonhosted.org/Sumatra/

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

54. Action points
Benchmarking/validation

55. Action points
Develop (under)graduate curriculum

56. My goal today
Flickr: http://farm4.staticflickr.com/3319/3265787219_bfbc654b5e_o.jpg