Coding & Best Practice in Programming in the NGS era

L
Lex NederbragtResearch Fellow at University of Oslo
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
Who am I
@lexnederbragt flxlexblog.wordpress.com
How I became a bioinformatician
2007: a grant
GS FLX from Roche/454
Genome Analyzer from Solexa/Illumina
?
Let’s try them out!
Specimen
• Planktothrix rubescens NIVA CYA 98
• Cyanobacteria
• (blue-green algae)
Planktothrix
Half a million reads
Average length 260 nt
10 million reads
33 nucleotides each
Perl
Planktothrix
Newbler SHARCGS
Assembly
Half a million reads
Average length 260 nt
10 million reads
33 nucleotides each
Atlantic cod genome project
850 million bases (Mbp )‘Wild-caught’
GS FLX from Roche/454
Atlantic cod genome project phase 1
Cod genome project phase 2
From Wikimedia commons, user Sagar Joshi
In summary
From flickr, user lesterpubliclibrary
Challenges in the next-generation sequencing era
High-throughput sequencing
Phase 1: more is better
Phase 2: smaller is better
Phase 3: single-molecule
Phase 4: nanopores
Democratization of sequencing
MinION
512 nanopores
150mb/hour
Up to 6 hours
$900
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?
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
Software
Constant stream of new software
http://wwwdev.ebi.ac.uk/fg/hts_mappers
88 short-read mappers
Software
Constant stream of new software
http://neidetcher.com/ubuntu_package_dependency.html
InstallationJudging quality
Wikimedia commons, user Thebestofall007
Do we need to be worried?
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?
Correctness of results
http://www.it.bton.ac.uk/staff/je/java/jewl/tutorial/tutorial.html
Reproducibility
doi:10.1038/sj.embor.7401143
A reproducibility crisis?
Reproducibility and reusability
http://upload.wikimedia.org/wikipedia/commons/4/48/Recycle.jpg
What it boils down to
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?
Diagnostic sequencing
Wikimedia commons, user Bill Branson
Diagnostic sequencing
Diagnostic sequencing
Solutions
Solutions
Flickr: http://farm4.staticflickr.com/3319/3265787219_bfbc654b5e_o.jpg Wikimedia commons
Best practices
10.1371/journal.pbio.1001745
Best practices
Automate repetitive tasks
Wikimedia commons, user Pzucchel
Best practices
Coding styles, variable naming etc
def test_seq:
def sequence_is_DNA:
Best practices
Use version control
https://www.atlassian.com/git/workflows
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
Best practices
test, test, test
def test_zero:
assert run_the_function(0) == 0
Assert x > 0, ”cannot handle negative numbers"
Best practices
Document well
Best practices
Collaborate
http://howdoitradestocks.com/wp-content/uploads/2011/12/share-ideas1.jpg
khmer, a 'case study'
khmer
Crusoe et al. doi: 10.6084/m9.figshare.979190Michael
Crusoe
Titus
Brown
khmer
https://github.com/ged-lab/2013-paper-ssspe
khmer
Integrated code
coverage analysis
The “GitHub Flow”
model of code review
Semantic
versioning
Continuous
integrationIntegration and
acceptance testing
Beyond best coding practices
Benchmarks
http://assemblathon.org/
Benchmarks
http://www.genome.org/cgi/doi/10.1101/gr.131383.111
Benchmarks
http://www.genomeinabottle.org/
~8300 10ug vials of DNA for NA12878
(Assembly) validation
(Assembly) validation
Assembly
doi:10.1186/1471-2105-15-126
Reproducibility ‘platforms’
usegalaxy.org
taverna.org.uk/
pythonhosted.org/Sumatra/
Action points
Action points
Attend a software Carpentry Boot Camp
http://software-carpentry.org/
Action points
Look for signs of best practice
Action points
Look for signs of best practice
during peer review
nature.com
Action points
Benchmarking/validation
Action points
Develop (under)graduate curriculum
My goal today
Flickr: http://farm4.staticflickr.com/3319/3265787219_bfbc654b5e_o.jpg
1 of 56

Recommended

NGS Applications I (UEB-UAT Bioinformatics Course - Session 2.1.2 - VHIR, Bar... by
NGS Applications I (UEB-UAT Bioinformatics Course - Session 2.1.2 - VHIR, Bar...NGS Applications I (UEB-UAT Bioinformatics Course - Session 2.1.2 - VHIR, Bar...
NGS Applications I (UEB-UAT Bioinformatics Course - Session 2.1.2 - VHIR, Bar...VHIR Vall d’Hebron Institut de Recerca
6.5K views32 slides
Next-generation sequencing from 2005 to 2020 by
Next-generation sequencing from 2005 to 2020Next-generation sequencing from 2005 to 2020
Next-generation sequencing from 2005 to 2020Christian Frech
12K views29 slides
I Jornada Actualización en Genética Reproductiva y Fertilidad by
I Jornada Actualización en Genética Reproductiva y Fertilidad I Jornada Actualización en Genética Reproductiva y Fertilidad
I Jornada Actualización en Genética Reproductiva y Fertilidad TECNALIA Research & Innovation
1.9K views30 slides
NGS: bioinformatic challenges by
NGS: bioinformatic challengesNGS: bioinformatic challenges
NGS: bioinformatic challengesLex Nederbragt
4.7K views50 slides
Making Use of NGS Data: From Reads to Trees and Annotations by
Making Use of NGS Data: From Reads to Trees and AnnotationsMaking Use of NGS Data: From Reads to Trees and Annotations
Making Use of NGS Data: From Reads to Trees and AnnotationsJoão André Carriço
1.3K views36 slides
Speeding up sequencing: Sequencing in an hour enables sample to answer in a w... by
Speeding up sequencing: Sequencing in an hour enables sample to answer in a w...Speeding up sequencing: Sequencing in an hour enables sample to answer in a w...
Speeding up sequencing: Sequencing in an hour enables sample to answer in a w...Thermo Fisher Scientific
2.7K views1 slide

More Related Content

What's hot

A decade into Next Generation Sequencing on marine non-model organisms: curre... by
A decade into Next Generation Sequencing on marine non-model organisms: curre...A decade into Next Generation Sequencing on marine non-model organisms: curre...
A decade into Next Generation Sequencing on marine non-model organisms: curre...Alexander Jueterbock
2K views49 slides
Microbiome Profiling with the Microbial Genomics Pro Suite by
Microbiome Profiling with the Microbial Genomics Pro SuiteMicrobiome Profiling with the Microbial Genomics Pro Suite
Microbiome Profiling with the Microbial Genomics Pro SuiteQIAGEN
3.7K views32 slides
Big data nebraska by
Big data nebraskaBig data nebraska
Big data nebraskaAdina Chuang Howe
542 views58 slides
Poster ESHG by
Poster ESHGPoster ESHG
Poster ESHGKirsten van Nimwegen
973 views1 slide
How to Standardise and Assemble Raw Data into Sequences: What Does it Mean fo... by
How to Standardise and Assemble Raw Data into Sequences: What Does it Mean fo...How to Standardise and Assemble Raw Data into Sequences: What Does it Mean fo...
How to Standardise and Assemble Raw Data into Sequences: What Does it Mean fo...Joseph Hughes
2.4K views21 slides
Next Generation Sequencing (NGS) in food safety-Game changer or just another ... by
Next Generation Sequencing (NGS) in food safety-Game changer or just another ...Next Generation Sequencing (NGS) in food safety-Game changer or just another ...
Next Generation Sequencing (NGS) in food safety-Game changer or just another ...ExternalEvents
4K views8 slides

What's hot(20)

A decade into Next Generation Sequencing on marine non-model organisms: curre... by Alexander Jueterbock
A decade into Next Generation Sequencing on marine non-model organisms: curre...A decade into Next Generation Sequencing on marine non-model organisms: curre...
A decade into Next Generation Sequencing on marine non-model organisms: curre...
Microbiome Profiling with the Microbial Genomics Pro Suite by QIAGEN
Microbiome Profiling with the Microbial Genomics Pro SuiteMicrobiome Profiling with the Microbial Genomics Pro Suite
Microbiome Profiling with the Microbial Genomics Pro Suite
QIAGEN3.7K views
How to Standardise and Assemble Raw Data into Sequences: What Does it Mean fo... by Joseph Hughes
How to Standardise and Assemble Raw Data into Sequences: What Does it Mean fo...How to Standardise and Assemble Raw Data into Sequences: What Does it Mean fo...
How to Standardise and Assemble Raw Data into Sequences: What Does it Mean fo...
Joseph Hughes2.4K views
Next Generation Sequencing (NGS) in food safety-Game changer or just another ... by ExternalEvents
Next Generation Sequencing (NGS) in food safety-Game changer or just another ...Next Generation Sequencing (NGS) in food safety-Game changer or just another ...
Next Generation Sequencing (NGS) in food safety-Game changer or just another ...
ExternalEvents4K views
Ernesto Picardi – Bioinformatica e genomica comparata: nuove strategie sperim... by eventi-ITBbari
Ernesto Picardi – Bioinformatica e genomica comparata: nuove strategie sperim...Ernesto Picardi – Bioinformatica e genomica comparata: nuove strategie sperim...
Ernesto Picardi – Bioinformatica e genomica comparata: nuove strategie sperim...
eventi-ITBbari3.7K views
BioChain Next Generation Sequencing Products by biochain
BioChain Next Generation Sequencing ProductsBioChain Next Generation Sequencing Products
BioChain Next Generation Sequencing Products
biochain816 views
Bioinformatics tools for the diagnostic laboratory - T.Seemann - Antimicrobi... by Torsten Seemann
Bioinformatics tools for the diagnostic laboratory -  T.Seemann - Antimicrobi...Bioinformatics tools for the diagnostic laboratory -  T.Seemann - Antimicrobi...
Bioinformatics tools for the diagnostic laboratory - T.Seemann - Antimicrobi...
Torsten Seemann3.8K views
2011 jeroen vanhoudt_ngs by Din Apellidos
2011 jeroen vanhoudt_ngs2011 jeroen vanhoudt_ngs
2011 jeroen vanhoudt_ngs
Din Apellidos4.2K views
White Paper: Next-Generation Genome Sequencing Using EMC Isilon Scale-Out NAS... by EMC
White Paper: Next-Generation Genome Sequencing Using EMC Isilon Scale-Out NAS...White Paper: Next-Generation Genome Sequencing Using EMC Isilon Scale-Out NAS...
White Paper: Next-Generation Genome Sequencing Using EMC Isilon Scale-Out NAS...
EMC3.1K views
Illumina-General-Overview-Q1-17 by Matthew Holguin
Illumina-General-Overview-Q1-17Illumina-General-Overview-Q1-17
Illumina-General-Overview-Q1-17
Matthew Holguin1.5K views
Rnaseq basics ngs_application1 by Yaoyu Wang
Rnaseq basics ngs_application1Rnaseq basics ngs_application1
Rnaseq basics ngs_application1
Yaoyu Wang5.3K views
20160219 - S. De Toffol - Dal Sanger al NGS nello studio delle mutazioni BRCA by Roberto Scarafia
20160219 - S. De Toffol -  Dal Sanger al NGS nello studio delle mutazioni BRCA �20160219 - S. De Toffol -  Dal Sanger al NGS nello studio delle mutazioni BRCA �
20160219 - S. De Toffol - Dal Sanger al NGS nello studio delle mutazioni BRCA
Roberto Scarafia2.6K views
The Next, Next Generation of Sequencing - From Semiconductor to Single Molecule by Justin Johnson
The Next, Next Generation of Sequencing - From Semiconductor to Single MoleculeThe Next, Next Generation of Sequencing - From Semiconductor to Single Molecule
The Next, Next Generation of Sequencing - From Semiconductor to Single Molecule
Justin Johnson2.7K views
Advances and Applications Enabled by Single Cell Technology by QIAGEN
Advances and Applications Enabled by Single Cell TechnologyAdvances and Applications Enabled by Single Cell Technology
Advances and Applications Enabled by Single Cell Technology
QIAGEN1.6K views
Next generation sequencing & microarray-- Genotypic Technology by Genotypic Technology
Next generation sequencing & microarray-- Genotypic TechnologyNext generation sequencing & microarray-- Genotypic Technology
Next generation sequencing & microarray-- Genotypic Technology
Knowing Your NGS Upstream: Alignment and Variants by Golden Helix Inc
Knowing Your NGS Upstream: Alignment and VariantsKnowing Your NGS Upstream: Alignment and Variants
Knowing Your NGS Upstream: Alignment and Variants
Golden Helix Inc5.9K views

Viewers also liked

Next generation sequencing by
Next generation sequencingNext generation sequencing
Next generation sequencingDayananda Salam
21.9K views25 slides
Next Gen Sequencing (NGS) Technology Overview by
Next Gen Sequencing (NGS) Technology OverviewNext Gen Sequencing (NGS) Technology Overview
Next Gen Sequencing (NGS) Technology OverviewDominic Suciu
48.1K views32 slides
NGS technologies - platforms and applications by
NGS technologies - platforms and applicationsNGS technologies - platforms and applications
NGS technologies - platforms and applicationsAGRF_Ltd
15.4K views38 slides
Ngs ppt by
Ngs pptNgs ppt
Ngs pptArcha Dave
58.1K views16 slides
Introduction to next generation sequencing by
Introduction to next generation sequencingIntroduction to next generation sequencing
Introduction to next generation sequencingVHIR Vall d’Hebron Institut de Recerca
115.1K views62 slides
NGS in cancer treatment by
NGS in cancer treatmentNGS in cancer treatment
NGS in cancer treatmentNur Suhaida
4.8K views15 slides

Viewers also liked(20)

Next generation sequencing by Dayananda Salam
Next generation sequencingNext generation sequencing
Next generation sequencing
Dayananda Salam21.9K views
Next Gen Sequencing (NGS) Technology Overview by Dominic Suciu
Next Gen Sequencing (NGS) Technology OverviewNext Gen Sequencing (NGS) Technology Overview
Next Gen Sequencing (NGS) Technology Overview
Dominic Suciu48.1K views
NGS technologies - platforms and applications by AGRF_Ltd
NGS technologies - platforms and applicationsNGS technologies - platforms and applications
NGS technologies - platforms and applications
AGRF_Ltd15.4K views
Ngs ppt by Archa Dave
Ngs pptNgs ppt
Ngs ppt
Archa Dave58.1K views
NGS in cancer treatment by Nur Suhaida
NGS in cancer treatmentNGS in cancer treatment
NGS in cancer treatment
Nur Suhaida4.8K views
Next Generation Sequencing & Transcriptome Analysis by Bastian Greshake
Next Generation Sequencing & Transcriptome AnalysisNext Generation Sequencing & Transcriptome Analysis
Next Generation Sequencing & Transcriptome Analysis
Bastian Greshake9.4K views
Overview of methods for variant calling from next-generation sequence data by Thomas Keane
Overview of methods for variant calling from next-generation sequence dataOverview of methods for variant calling from next-generation sequence data
Overview of methods for variant calling from next-generation sequence data
Thomas Keane9.5K views
Introduction to NGS by cursoNGS
Introduction to NGSIntroduction to NGS
Introduction to NGS
cursoNGS7.6K views
Making your science powerful : an introduction to NGS experimental design by jelena121
Making your science powerful : an introduction to NGS experimental designMaking your science powerful : an introduction to NGS experimental design
Making your science powerful : an introduction to NGS experimental design
jelena1214.3K views
NEXT GENERATION SEQUENCING by Bilal Nizami
NEXT GENERATION SEQUENCINGNEXT GENERATION SEQUENCING
NEXT GENERATION SEQUENCING
Bilal Nizami72K views
NGS for Infectious Disease Diagnostics: An Opportunity for Growth by Alira Health
NGS for Infectious Disease Diagnostics: An Opportunity for Growth NGS for Infectious Disease Diagnostics: An Opportunity for Growth
NGS for Infectious Disease Diagnostics: An Opportunity for Growth
Alira Health 4.6K views
Computational infrastructure for NGS data analysis by cursoNGS
Computational infrastructure for NGS data analysisComputational infrastructure for NGS data analysis
Computational infrastructure for NGS data analysis
cursoNGS4.6K views
Step by Step, from Liquid Biopsy to a Genomic Biomarker: Liquid Biopsy Series... by QIAGEN
Step by Step, from Liquid Biopsy to a Genomic Biomarker: Liquid Biopsy Series...Step by Step, from Liquid Biopsy to a Genomic Biomarker: Liquid Biopsy Series...
Step by Step, from Liquid Biopsy to a Genomic Biomarker: Liquid Biopsy Series...
QIAGEN3.3K views
Digital RNAseq Technology Introduction: Digital RNAseq Webinar Part 1 by QIAGEN
Digital RNAseq Technology Introduction: Digital RNAseq Webinar Part 1Digital RNAseq Technology Introduction: Digital RNAseq Webinar Part 1
Digital RNAseq Technology Introduction: Digital RNAseq Webinar Part 1
QIAGEN3.2K views
Advanced NGS Data Analysis & Interpretation- BGW + IVA: NGS Tech Overview Web... by QIAGEN
Advanced NGS Data Analysis & Interpretation- BGW + IVA: NGS Tech Overview Web...Advanced NGS Data Analysis & Interpretation- BGW + IVA: NGS Tech Overview Web...
Advanced NGS Data Analysis & Interpretation- BGW + IVA: NGS Tech Overview Web...
QIAGEN4.5K views
“Next-Generation Sequencing (NGS) Global Market – Forecast To 2022” by Vinay Shiva Prasad
“Next-Generation Sequencing (NGS) Global Market  – Forecast To 2022”“Next-Generation Sequencing (NGS) Global Market  – Forecast To 2022”
“Next-Generation Sequencing (NGS) Global Market – Forecast To 2022”
Vinay Shiva Prasad922 views

Similar to Coding & Best Practice in Programming in the NGS era

2013 pag-equine-workshop by
2013 pag-equine-workshop2013 pag-equine-workshop
2013 pag-equine-workshopc.titus.brown
1.4K views47 slides
Lab2_3_Lecture_DNA_PCR (3).pptx by
Lab2_3_Lecture_DNA_PCR (3).pptxLab2_3_Lecture_DNA_PCR (3).pptx
Lab2_3_Lecture_DNA_PCR (3).pptxkarlos64
4 views41 slides
Use of bio-informatic tools in bacterial genetics by
Use of bio-informatic tools in bacterial geneticsUse of bio-informatic tools in bacterial genetics
Use of bio-informatic tools in bacterial geneticsDebtanu Chakraborty
575 views47 slides
Brochure Algae Engineering Kits by
Brochure Algae Engineering KitsBrochure Algae Engineering Kits
Brochure Algae Engineering KitsDaniel Schroen, PhD
162 views12 slides
Health, Data Analytics and Decision Support by
Health, Data Analytics and Decision SupportHealth, Data Analytics and Decision Support
Health, Data Analytics and Decision Supportimec
825 views29 slides
Submitted sequence (strains) by
Submitted sequence (strains)Submitted sequence (strains)
Submitted sequence (strains)Syeda Masoom Fatima
82 views19 slides

Similar to Coding & Best Practice in Programming in the NGS era(20)

2013 pag-equine-workshop by c.titus.brown
2013 pag-equine-workshop2013 pag-equine-workshop
2013 pag-equine-workshop
c.titus.brown1.4K views
Lab2_3_Lecture_DNA_PCR (3).pptx by karlos64
Lab2_3_Lecture_DNA_PCR (3).pptxLab2_3_Lecture_DNA_PCR (3).pptx
Lab2_3_Lecture_DNA_PCR (3).pptx
karlos644 views
Use of bio-informatic tools in bacterial genetics by Debtanu Chakraborty
Use of bio-informatic tools in bacterial geneticsUse of bio-informatic tools in bacterial genetics
Use of bio-informatic tools in bacterial genetics
Health, Data Analytics and Decision Support by imec
Health, Data Analytics and Decision SupportHealth, Data Analytics and Decision Support
Health, Data Analytics and Decision Support
imec825 views
The Human Genome Project - Part I by hhalhaddad
The Human Genome Project - Part IThe Human Genome Project - Part I
The Human Genome Project - Part I
hhalhaddad4.7K views
Turn Away from Traditional Tethering and Towards a Better Method for Data Col... by InsideScientific
Turn Away from Traditional Tethering and Towards a Better Method for Data Col...Turn Away from Traditional Tethering and Towards a Better Method for Data Col...
Turn Away from Traditional Tethering and Towards a Better Method for Data Col...
InsideScientific1.1K views
Molecular Biology Intro.pdf by ssuser432659
Molecular Biology Intro.pdfMolecular Biology Intro.pdf
Molecular Biology Intro.pdf
ssuser43265960 views
Diversity Diversity Diversity Diversity .... by Jonathan Eisen
Diversity Diversity Diversity Diversity ....Diversity Diversity Diversity Diversity ....
Diversity Diversity Diversity Diversity ....
Jonathan Eisen1.9K views
Wild Strawberry: An emerging model for ecological and evolutionary genomics by Aaron Liston
Wild Strawberry: An emerging model for ecological and evolutionary genomicsWild Strawberry: An emerging model for ecological and evolutionary genomics
Wild Strawberry: An emerging model for ecological and evolutionary genomics
Aaron Liston2K views
Prokka - rapid bacterial genome annotation - ABPHM 2013 by Torsten Seemann
Prokka - rapid bacterial genome annotation - ABPHM 2013Prokka - rapid bacterial genome annotation - ABPHM 2013
Prokka - rapid bacterial genome annotation - ABPHM 2013
Torsten Seemann3.9K views
Genomic Cytometry: Using Multi-Omic Approaches to Increase Dimensionality in ... by Robert (Rob) Salomon
Genomic Cytometry: Using Multi-Omic Approaches to Increase Dimensionality in ...Genomic Cytometry: Using Multi-Omic Approaches to Increase Dimensionality in ...
Genomic Cytometry: Using Multi-Omic Approaches to Increase Dimensionality in ...
US2TS presentation on Gene Ontology by Chris Mungall
US2TS presentation on Gene OntologyUS2TS presentation on Gene Ontology
US2TS presentation on Gene Ontology
Chris Mungall358 views
DNA sequencing: rapid improvements and their implications by Jeffrey Funk
DNA sequencing: rapid improvements and their implicationsDNA sequencing: rapid improvements and their implications
DNA sequencing: rapid improvements and their implications
Jeffrey Funk11K views
Epigenetic and Environmental Influences on the Shellfish Immune Response by sr320
Epigenetic and Environmental Influences on the Shellfish Immune ResponseEpigenetic and Environmental Influences on the Shellfish Immune Response
Epigenetic and Environmental Influences on the Shellfish Immune Response
sr3202.3K views

More from Lex Nederbragt

Why of version control by
Why of version controlWhy of version control
Why of version controlLex Nederbragt
2.4K views17 slides
Assembly: before and after by
Assembly: before and afterAssembly: before and after
Assembly: before and afterLex Nederbragt
5.6K views50 slides
Improving and validating the Atlantic Cod genome assembly using PacBio by
Improving and validating the Atlantic Cod genome assembly using PacBioImproving and validating the Atlantic Cod genome assembly using PacBio
Improving and validating the Atlantic Cod genome assembly using PacBioLex Nederbragt
5.1K views54 slides
Repeat after me: Is our research reproducible (enough)? by
Repeat after me: Is our research reproducible (enough)? Repeat after me: Is our research reproducible (enough)?
Repeat after me: Is our research reproducible (enough)? Lex Nederbragt
1.8K views23 slides
A different kettle of fish entirely: bioinformatic challenges and solutions f... by
A different kettle of fish entirely: bioinformatic challenges and solutions f...A different kettle of fish entirely: bioinformatic challenges and solutions f...
A different kettle of fish entirely: bioinformatic challenges and solutions f...Lex Nederbragt
7.4K views66 slides
Combining PacBio with short read technology for improved de novo genome assembly by
Combining PacBio with short read technology for improved de novo genome assemblyCombining PacBio with short read technology for improved de novo genome assembly
Combining PacBio with short read technology for improved de novo genome assemblyLex Nederbragt
5.6K views56 slides

More from Lex Nederbragt(12)

Assembly: before and after by Lex Nederbragt
Assembly: before and afterAssembly: before and after
Assembly: before and after
Lex Nederbragt5.6K views
Improving and validating the Atlantic Cod genome assembly using PacBio by Lex Nederbragt
Improving and validating the Atlantic Cod genome assembly using PacBioImproving and validating the Atlantic Cod genome assembly using PacBio
Improving and validating the Atlantic Cod genome assembly using PacBio
Lex Nederbragt5.1K views
Repeat after me: Is our research reproducible (enough)? by Lex Nederbragt
Repeat after me: Is our research reproducible (enough)? Repeat after me: Is our research reproducible (enough)?
Repeat after me: Is our research reproducible (enough)?
Lex Nederbragt1.8K views
A different kettle of fish entirely: bioinformatic challenges and solutions f... by Lex Nederbragt
A different kettle of fish entirely: bioinformatic challenges and solutions f...A different kettle of fish entirely: bioinformatic challenges and solutions f...
A different kettle of fish entirely: bioinformatic challenges and solutions f...
Lex Nederbragt7.4K views
Combining PacBio with short read technology for improved de novo genome assembly by Lex Nederbragt
Combining PacBio with short read technology for improved de novo genome assemblyCombining PacBio with short read technology for improved de novo genome assembly
Combining PacBio with short read technology for improved de novo genome assembly
Lex Nederbragt5.6K views
Updated: New High Throughput Sequencing technologies at the Norwegian Sequenc... by Lex Nederbragt
Updated: New High Throughput Sequencing technologies at the Norwegian Sequenc...Updated: New High Throughput Sequencing technologies at the Norwegian Sequenc...
Updated: New High Throughput Sequencing technologies at the Norwegian Sequenc...
Lex Nederbragt3.3K views
New High Throughput Sequencing technologies at the Norwegian Sequencing Centr... by Lex Nederbragt
New High Throughput Sequencing technologies at the Norwegian Sequencing Centr...New High Throughput Sequencing technologies at the Norwegian Sequencing Centr...
New High Throughput Sequencing technologies at the Norwegian Sequencing Centr...
Lex Nederbragt5.1K views
How and why I use blogging by Lex Nederbragt
How and why I use bloggingHow and why I use blogging
How and why I use blogging
Lex Nederbragt1.1K views
How to sequence a large eukaryotic genome by Lex Nederbragt
How to sequence a large eukaryotic genomeHow to sequence a large eukaryotic genome
How to sequence a large eukaryotic genome
Lex Nederbragt14.8K views

Recently uploaded

Gel Filtration or Permeation Chromatography by
Gel Filtration or Permeation ChromatographyGel Filtration or Permeation Chromatography
Gel Filtration or Permeation ChromatographyPoonam Aher Patil
12 views15 slides
GLUCONEOGENESIS Presentation.pptx by
GLUCONEOGENESIS Presentation.pptxGLUCONEOGENESIS Presentation.pptx
GLUCONEOGENESIS Presentation.pptxGunjanBaisla
6 views19 slides
Major important agricultural crop Diseases list by
Major important agricultural crop Diseases listMajor important agricultural crop Diseases list
Major important agricultural crop Diseases listYuvarajYuva27
9 views21 slides
ELECTRON TRANSPORT CHAIN by
ELECTRON TRANSPORT CHAINELECTRON TRANSPORT CHAIN
ELECTRON TRANSPORT CHAINDEEKSHA RANI
26 views16 slides
DNA manipulation Enzymes 2.pdf by
DNA manipulation Enzymes 2.pdfDNA manipulation Enzymes 2.pdf
DNA manipulation Enzymes 2.pdfNetHelix
6 views42 slides
HIGH PERFORMANCE THIN LAYER CHROMATOGRAPHY by
HIGH PERFORMANCE THIN LAYER CHROMATOGRAPHYHIGH PERFORMANCE THIN LAYER CHROMATOGRAPHY
HIGH PERFORMANCE THIN LAYER CHROMATOGRAPHYPoonam Aher Patil
9 views42 slides

Recently uploaded(20)

Gel Filtration or Permeation Chromatography by Poonam Aher Patil
Gel Filtration or Permeation ChromatographyGel Filtration or Permeation Chromatography
Gel Filtration or Permeation Chromatography
GLUCONEOGENESIS Presentation.pptx by GunjanBaisla
GLUCONEOGENESIS Presentation.pptxGLUCONEOGENESIS Presentation.pptx
GLUCONEOGENESIS Presentation.pptx
GunjanBaisla6 views
Major important agricultural crop Diseases list by YuvarajYuva27
Major important agricultural crop Diseases listMajor important agricultural crop Diseases list
Major important agricultural crop Diseases list
YuvarajYuva279 views
ELECTRON TRANSPORT CHAIN by DEEKSHA RANI
ELECTRON TRANSPORT CHAINELECTRON TRANSPORT CHAIN
ELECTRON TRANSPORT CHAIN
DEEKSHA RANI26 views
DNA manipulation Enzymes 2.pdf by NetHelix
DNA manipulation Enzymes 2.pdfDNA manipulation Enzymes 2.pdf
DNA manipulation Enzymes 2.pdf
NetHelix6 views
KeyAI. Solving a math problem to recover lost crypto assets. by RFID INC
KeyAI. Solving a math problem to recover lost crypto assets.KeyAI. Solving a math problem to recover lost crypto assets.
KeyAI. Solving a math problem to recover lost crypto assets.
RFID INC35 views
2. Natural Sciences and Technology Author Siyavula.pdf by ssuser821efa
2. Natural Sciences and Technology Author Siyavula.pdf2. Natural Sciences and Technology Author Siyavula.pdf
2. Natural Sciences and Technology Author Siyavula.pdf
ssuser821efa13 views
Study on Drug Drug Interaction Through Prescription Analysis of Type II Diabe... by Anmol Vishnu Gupta
Study on Drug Drug Interaction Through Prescription Analysis of Type II Diabe...Study on Drug Drug Interaction Through Prescription Analysis of Type II Diabe...
Study on Drug Drug Interaction Through Prescription Analysis of Type II Diabe...
Best Hybrid Event Platform.pptx by Harriet Davis
Best Hybrid Event Platform.pptxBest Hybrid Event Platform.pptx
Best Hybrid Event Platform.pptx
Harriet Davis11 views
Towards Error-Corrected Quantum Computing with Neutral Atoms by Yuval Boger
Towards Error-Corrected Quantum Computing with Neutral AtomsTowards Error-Corrected Quantum Computing with Neutral Atoms
Towards Error-Corrected Quantum Computing with Neutral Atoms
Yuval Boger5 views
A giant thin stellar stream in the Coma Galaxy Cluster by Sérgio Sacani
A giant thin stellar stream in the Coma Galaxy ClusterA giant thin stellar stream in the Coma Galaxy Cluster
A giant thin stellar stream in the Coma Galaxy Cluster
Sérgio Sacani25 views
Non Aqueous titration: Definition, Principle and Application by Poonam Aher Patil
Non Aqueous titration: Definition, Principle and ApplicationNon Aqueous titration: Definition, Principle and Application
Non Aqueous titration: Definition, Principle and Application
COMPLEXOMETRIC TITRATION OR CHEALATOMETRIC TITRATION by Poonam Aher Patil
COMPLEXOMETRIC TITRATION OR CHEALATOMETRIC TITRATIONCOMPLEXOMETRIC TITRATION OR CHEALATOMETRIC TITRATION
COMPLEXOMETRIC TITRATION OR CHEALATOMETRIC TITRATION
Poonam Aher Patil267 views
Generative AI to Accelerate Discovery of Materials by Deakin University
Generative AI to Accelerate Discovery of MaterialsGenerative AI to Accelerate Discovery of Materials
Generative AI to Accelerate Discovery of Materials
Presentation on experimental laboratory animal- Hamster by Kanika13641
Presentation on experimental laboratory animal- HamsterPresentation on experimental laboratory animal- Hamster
Presentation on experimental laboratory animal- Hamster
Kanika136418 views
Heavy Tails Workshop NeurIPS2023.pdf by Charles Martin
Heavy Tails Workshop NeurIPS2023.pdfHeavy Tails Workshop NeurIPS2023.pdf
Heavy Tails Workshop NeurIPS2023.pdf
Charles Martin96 views
Evaluation and Standardization of the Marketed Polyherbal drug Patanjali Divy... by Anmol Vishnu Gupta
Evaluation and Standardization of the Marketed Polyherbal drug Patanjali Divy...Evaluation and Standardization of the Marketed Polyherbal drug Patanjali Divy...
Evaluation and Standardization of the Marketed Polyherbal drug Patanjali Divy...

Coding & Best Practice in Programming in the NGS era

Editor's Notes

  1. pre-merge code reviews.pair programming issue tracking
  2. develop the reference materials, reference data, and reference methods needed to assess performance of human genome sequencing.