SlideShare a Scribd company logo
Understanding the reference assembly
Valerie Schneider
NCBI
26 October 2016
http://www.biorxiv.org/content/early/2016/08/30/072116
Dilthey et al.Paten et al.
Scientific Models
• Distinguishing features of the human reference
assembly
• Implications for genomic analyses and tools
• Where do you get assembly-relevant data?
Outline
Understanding the reference assembly: CSHL Hackathon
Assembly Basics
Sanger-seq’d, clone based assembly BAC insert
BAC vector
Shotgun sequence clone
Assemble
GAPS
Finish
Minimal Tiling Path
Define switch points for adjacent components
(haploid mosaic)
Most contiguous
Highest sequence quality
Today’s reference assembly does not represent:
1.The most common allele
2.The longest allele
3.The ancestral allele
Assembly Basics
It represents the sequence available from the HGP
GRC Assembly Model
Sequences from haplotype 1
Sequences from haplotype 2
Old Assembly model: compress into a consensus
Current Assembly model: represent both haplotypes
many
Assembly (e.g. GRCh38)
Primary
Assembly
Unit
Non-nuclear
assembly unit
(e.g. MT)
PAR
Genomic
Region
(MHC)
Genomic
Region
(UGT2B17)
Genomic
Region
(MAPT)
Church et al., PLoS Biol. 2011 Jul;9(7):e1001091
GRC Assembly Model
ALT
2
ALT
3
ALT
4
ALT
5
ALT
6
ALT
7
ALT
1
The alignments of the alternate loci scaffolds to the
chromosomes are an integral part of the assembly
and can be downloaded from GenBank with the
assembly sequences
Assembly (e.g. GRCh38.p1)
Primary
Assembly
Unit
Non-nuclear
assembly unit
(e.g. MT)
ALT
1
ALT
2
ALT
3
ALT
4
ALT
5
ALT
6
ALT
7
PAR
Genomic
Region
(MHC)
Genomic
Region
(UGT2B17)
Genomic
Region
(MAPT)
Church et al., PLoS Biol. 2011 Jul;9(7):e1001091
Patches
Genomic
Region
(ABO)
Genomic
Region
(FOXO6)
Genomic
Region
(FCGBP)
GRC Assembly Model
Patches
FIX NOVEL
SCAFFOLD STATUS AT NEXT
MAJOR ASSEMBLY RELEASE
ALT
LOCI
--
(integrated)
Treat as:
Allelic
Treat as:
Preferred
1q32 1q21 1p21
Dennis et al., 2012
GRC Assembly Model
GRC: Assembly Model
GRCh38
• 178 regions with alt loci: 2% of chromosome
sequence (61.9 Mb)
• 261 Alt Loci: 3.6 Mb novel sequence relative to
chromosomes
GRCh38.p9
• 96 Patches: >1 Mb novel sequence
• 48 FIX
• 48 NOVEL
GRC: Assembly Model
GRCh38: Alt Loci
Alignment Legend
no alignmentmismatchdeletion
chromosome
alt/patch
reads On-target alignment
Off-target alignments
(n=122,922)
GRCh38: Alt LociPLoS Biol. 2011 Jul;9(7):e1001091
Anatomy of an alt
Anatomy of an alt
AC012314.8
CU151838.1
ALT LOCI
AC012314.8
AC245052.3 CHR. 19
Due to anchor components, alternate loci contain some sequence
that is redundant to the primary assembly unit
GRCh38 Model Centromeres
Karen Miga (Kent Lab, UCSC)
GRCh38 Model Centromeres
WGS WGS WGS
GRCh38 Centromeres
Miga et al., Genome Res. 2014 Apr;24(4):697-707
GRCh38: Where’s the data?
GRCh38: Where’s the data?
GRCh38 Sequences for alignment pipelines
GRCh38: Where’s the data?
Assembly Sequence and Statistics Reports
GRCh38: Where’s the data?
GRCh38: Where’s the data?
GRCh38: Where’s the data?
Assembly Regions Report: Alts, Patches and Centromeres
GRCh38: Where’s the data?
Understanding the reference assembly: CSHL Hackathon
GRCh38: Where’s the data?
GRCh38: Where’s the data?
Accessing the Datahttps://genomereference.org
Accessing the Datahttps://genomereference.org
Dumped daily
Frozen mappings to
prior assembly
versions in GFF3
Accessing the Datahttps://genomereference.org
Mapped to latest GRCh38 and GRCh37.p13
Accessing the Datahttps://genomereference.org
GRCh38 Collaborators
• NCBI RefSeq and gpipe annotation team
• Havana annotators
• Karen Miga
• David Schwartz
• Steve Goldstein
• Mario Caceres
• Giulio Genovese
• Jeff Kidd
• Peter Lansdorp
• Mark Hills
• David Page
• Jim Knight
• Stephan Schuster
• 1000 Genomes
GRC SAB
• Rick Myers
• Granger Sutton
• Evan Eichler
• Jim Kent
• Roderic Guigo
• Carol Bult
• Derek Stemple
• Jan Korbel
• Liz Worthey
• Matthew Hurles
• Richard Gibbs
GRC Creditshttps://genomereference.org
Alt Loci: Informatics Challenges
Masks and alt aware aligners reduce the incidence of
ambiguous alignments observed when aligning reads to
the full assembly
Mask1: mask chr for fix patches, scaffold for novel/alts. Mask2: mask only on scaffolds
Simulated Reads
GRCh38: Alt Loci
The Changing Reference
The Changing Reference
Dilthey et al.Paten et al.
The Changing Reference
• Distinguishing features of the human reference
assembly
• Implications for genomic analyses and tools
• Where do you get assembly-relevant data?
Outline

More Related Content

What's hot

Getting the most from the reference assembly
Getting the most from the reference assemblyGetting the most from the reference assembly
Getting the most from the reference assembly
Genome Reference Consortium
 
agbt 2016 workshop church
agbt 2016 workshop churchagbt 2016 workshop church
agbt 2016 workshop church
Genome Reference Consortium
 
ABGT 2016 Workshop Schneider
ABGT 2016 Workshop SchneiderABGT 2016 Workshop Schneider
ABGT 2016 Workshop Schneider
Genome Reference Consortium
 
Alignment Approaches II: Long Reads
Alignment Approaches II: Long ReadsAlignment Approaches II: Long Reads
Alignment Approaches II: Long Reads
Genome Reference Consortium
 
GRCWorkshop_geval_1KG_slides
GRCWorkshop_geval_1KG_slidesGRCWorkshop_geval_1KG_slides
GRCWorkshop_geval_1KG_slides
Genome Reference Consortium
 
Ashg2015 grc-pruitt
Ashg2015 grc-pruittAshg2015 grc-pruitt
Ashg2015 grc-pruitt
Genome Reference Consortium
 
Variant Calling II
Variant Calling IIVariant Calling II
Variant Calling II
Genome Reference Consortium
 
Grc workshop agbt2015_tg
Grc workshop agbt2015_tgGrc workshop agbt2015_tg
Grc workshop agbt2015_tg
Genome Reference Consortium
 
Creating Reference-Grade Human Genome Assemblies
Creating Reference-Grade Human Genome AssembliesCreating Reference-Grade Human Genome Assemblies
Creating Reference-Grade Human Genome Assemblies
Genome Reference Consortium
 
Ashg2017 workshop tg
Ashg2017 workshop tgAshg2017 workshop tg
Ashg2017 workshop tg
Genome Reference Consortium
 
agbt 2016 workshop lindsay
agbt 2016 workshop lindsayagbt 2016 workshop lindsay
agbt 2016 workshop lindsay
Genome Reference Consortium
 
Grc ashg2015 workshop_mudge
Grc ashg2015 workshop_mudgeGrc ashg2015 workshop_mudge
Grc ashg2015 workshop_mudge
Genome Reference Consortium
 
hg19 (GRCh37) vs. hg38 (GRCh38)
hg19 (GRCh37) vs. hg38 (GRCh38)hg19 (GRCh37) vs. hg38 (GRCh38)
hg19 (GRCh37) vs. hg38 (GRCh38)
Shaojun Xie
 
Schneider_AGBT2014
Schneider_AGBT2014Schneider_AGBT2014
Schneider_AGBT2014
vaschn
 
Previewing GRCm39: Assembly Updates from the GRC
Previewing GRCm39: Assembly Updates from the GRCPreviewing GRCm39: Assembly Updates from the GRC
Previewing GRCm39: Assembly Updates from the GRC
Genome Reference Consortium
 
AGBT2017 Reference Workshop: Lindsay
AGBT2017 Reference Workshop: LindsayAGBT2017 Reference Workshop: Lindsay
AGBT2017 Reference Workshop: Lindsay
Genome Reference Consortium
 
Explaining the assembly model
Explaining the assembly modelExplaining the assembly model
Explaining the assembly model
Genome Reference Consortium
 
AGBT2017 Reference Workshop: Schneider
AGBT2017 Reference Workshop: SchneiderAGBT2017 Reference Workshop: Schneider
AGBT2017 Reference Workshop: Schneider
Genome Reference Consortium
 
Ashg2017 workshop schneider
Ashg2017 workshop schneiderAshg2017 workshop schneider
Ashg2017 workshop schneider
Genome Reference Consortium
 
Haplotype resolved structural variation assembly with long reads
Haplotype resolved structural variation assembly with long readsHaplotype resolved structural variation assembly with long reads
Haplotype resolved structural variation assembly with long reads
Genome Reference Consortium
 

What's hot (20)

Getting the most from the reference assembly
Getting the most from the reference assemblyGetting the most from the reference assembly
Getting the most from the reference assembly
 
agbt 2016 workshop church
agbt 2016 workshop churchagbt 2016 workshop church
agbt 2016 workshop church
 
ABGT 2016 Workshop Schneider
ABGT 2016 Workshop SchneiderABGT 2016 Workshop Schneider
ABGT 2016 Workshop Schneider
 
Alignment Approaches II: Long Reads
Alignment Approaches II: Long ReadsAlignment Approaches II: Long Reads
Alignment Approaches II: Long Reads
 
GRCWorkshop_geval_1KG_slides
GRCWorkshop_geval_1KG_slidesGRCWorkshop_geval_1KG_slides
GRCWorkshop_geval_1KG_slides
 
Ashg2015 grc-pruitt
Ashg2015 grc-pruittAshg2015 grc-pruitt
Ashg2015 grc-pruitt
 
Variant Calling II
Variant Calling IIVariant Calling II
Variant Calling II
 
Grc workshop agbt2015_tg
Grc workshop agbt2015_tgGrc workshop agbt2015_tg
Grc workshop agbt2015_tg
 
Creating Reference-Grade Human Genome Assemblies
Creating Reference-Grade Human Genome AssembliesCreating Reference-Grade Human Genome Assemblies
Creating Reference-Grade Human Genome Assemblies
 
Ashg2017 workshop tg
Ashg2017 workshop tgAshg2017 workshop tg
Ashg2017 workshop tg
 
agbt 2016 workshop lindsay
agbt 2016 workshop lindsayagbt 2016 workshop lindsay
agbt 2016 workshop lindsay
 
Grc ashg2015 workshop_mudge
Grc ashg2015 workshop_mudgeGrc ashg2015 workshop_mudge
Grc ashg2015 workshop_mudge
 
hg19 (GRCh37) vs. hg38 (GRCh38)
hg19 (GRCh37) vs. hg38 (GRCh38)hg19 (GRCh37) vs. hg38 (GRCh38)
hg19 (GRCh37) vs. hg38 (GRCh38)
 
Schneider_AGBT2014
Schneider_AGBT2014Schneider_AGBT2014
Schneider_AGBT2014
 
Previewing GRCm39: Assembly Updates from the GRC
Previewing GRCm39: Assembly Updates from the GRCPreviewing GRCm39: Assembly Updates from the GRC
Previewing GRCm39: Assembly Updates from the GRC
 
AGBT2017 Reference Workshop: Lindsay
AGBT2017 Reference Workshop: LindsayAGBT2017 Reference Workshop: Lindsay
AGBT2017 Reference Workshop: Lindsay
 
Explaining the assembly model
Explaining the assembly modelExplaining the assembly model
Explaining the assembly model
 
AGBT2017 Reference Workshop: Schneider
AGBT2017 Reference Workshop: SchneiderAGBT2017 Reference Workshop: Schneider
AGBT2017 Reference Workshop: Schneider
 
Ashg2017 workshop schneider
Ashg2017 workshop schneiderAshg2017 workshop schneider
Ashg2017 workshop schneider
 
Haplotype resolved structural variation assembly with long reads
Haplotype resolved structural variation assembly with long readsHaplotype resolved structural variation assembly with long reads
Haplotype resolved structural variation assembly with long reads
 

Viewers also liked

AGBT2017 Reference Workshop: Fulton
AGBT2017 Reference Workshop: FultonAGBT2017 Reference Workshop: Fulton
AGBT2017 Reference Workshop: Fulton
Genome Reference Consortium
 
Variation reference graphs and the variation graph toolkit vg
Variation reference graphs and the variation graph toolkit vgVariation reference graphs and the variation graph toolkit vg
Variation reference graphs and the variation graph toolkit vg
Genome Reference Consortium
 
The Transforming Genetic Medicine Initiative (TGMI)
The Transforming Genetic Medicine Initiative (TGMI)The Transforming Genetic Medicine Initiative (TGMI)
The Transforming Genetic Medicine Initiative (TGMI)
Genome Reference Consortium
 
Graph and assembly strategies for the MHC and ribosomal DNA regions
Graph and assembly strategies for the MHC and ribosomal DNA regionsGraph and assembly strategies for the MHC and ribosomal DNA regions
Graph and assembly strategies for the MHC and ribosomal DNA regions
Genome Reference Consortium
 
ClinVar: Getting the most from the reference assembly and reference materials
ClinVar: Getting the most from the reference assembly and reference materialsClinVar: Getting the most from the reference assembly and reference materials
ClinVar: Getting the most from the reference assembly and reference materials
Genome Reference Consortium
 
Everyday de novo diploid assembly
Everyday de novo diploid assemblyEveryday de novo diploid assembly
Everyday de novo diploid assembly
Genome Reference Consortium
 
Genome in a Bottle
Genome in a BottleGenome in a Bottle
Genome in a Bottle
Genome Reference Consortium
 
Exploiting long read sequencing technology to build a substantially improved ...
Exploiting long read sequencing technology to build a substantially improved ...Exploiting long read sequencing technology to build a substantially improved ...
Exploiting long read sequencing technology to build a substantially improved ...
Genome Reference Consortium
 
Everyday de novo assembly
Everyday de novo assemblyEveryday de novo assembly
Everyday de novo assembly
Genome Reference Consortium
 
AGBT 2016 Workshop Magrini
AGBT 2016 Workshop MagriniAGBT 2016 Workshop Magrini
AGBT 2016 Workshop Magrini
Genome Reference Consortium
 
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
BITS
 
Microarray data and pathway analysis: example from the bench
Microarray data and pathway analysis: example from the benchMicroarray data and pathway analysis: example from the bench
Microarray data and pathway analysis: example from the bench
Maté Ongenaert
 
RNA-seq for DE analysis: the biology behind observed changes - part 6
RNA-seq for DE analysis: the biology behind observed changes - part 6RNA-seq for DE analysis: the biology behind observed changes - part 6
RNA-seq for DE analysis: the biology behind observed changes - part 6
BITS
 
Functional And Pathway Analysis 2010
Functional And Pathway Analysis 2010Functional And Pathway Analysis 2010
Functional And Pathway Analysis 2010
Stewart MacArthur
 
RNA-seq for DE analysis: detecting differential expression - part 5
RNA-seq for DE analysis: detecting differential expression - part 5RNA-seq for DE analysis: detecting differential expression - part 5
RNA-seq for DE analysis: detecting differential expression - part 5
BITS
 

Viewers also liked (15)

AGBT2017 Reference Workshop: Fulton
AGBT2017 Reference Workshop: FultonAGBT2017 Reference Workshop: Fulton
AGBT2017 Reference Workshop: Fulton
 
Variation reference graphs and the variation graph toolkit vg
Variation reference graphs and the variation graph toolkit vgVariation reference graphs and the variation graph toolkit vg
Variation reference graphs and the variation graph toolkit vg
 
The Transforming Genetic Medicine Initiative (TGMI)
The Transforming Genetic Medicine Initiative (TGMI)The Transforming Genetic Medicine Initiative (TGMI)
The Transforming Genetic Medicine Initiative (TGMI)
 
Graph and assembly strategies for the MHC and ribosomal DNA regions
Graph and assembly strategies for the MHC and ribosomal DNA regionsGraph and assembly strategies for the MHC and ribosomal DNA regions
Graph and assembly strategies for the MHC and ribosomal DNA regions
 
ClinVar: Getting the most from the reference assembly and reference materials
ClinVar: Getting the most from the reference assembly and reference materialsClinVar: Getting the most from the reference assembly and reference materials
ClinVar: Getting the most from the reference assembly and reference materials
 
Everyday de novo diploid assembly
Everyday de novo diploid assemblyEveryday de novo diploid assembly
Everyday de novo diploid assembly
 
Genome in a Bottle
Genome in a BottleGenome in a Bottle
Genome in a Bottle
 
Exploiting long read sequencing technology to build a substantially improved ...
Exploiting long read sequencing technology to build a substantially improved ...Exploiting long read sequencing technology to build a substantially improved ...
Exploiting long read sequencing technology to build a substantially improved ...
 
Everyday de novo assembly
Everyday de novo assemblyEveryday de novo assembly
Everyday de novo assembly
 
AGBT 2016 Workshop Magrini
AGBT 2016 Workshop MagriniAGBT 2016 Workshop Magrini
AGBT 2016 Workshop Magrini
 
BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1BITS: UCSC genome browser - Part 1
BITS: UCSC genome browser - Part 1
 
Microarray data and pathway analysis: example from the bench
Microarray data and pathway analysis: example from the benchMicroarray data and pathway analysis: example from the bench
Microarray data and pathway analysis: example from the bench
 
RNA-seq for DE analysis: the biology behind observed changes - part 6
RNA-seq for DE analysis: the biology behind observed changes - part 6RNA-seq for DE analysis: the biology behind observed changes - part 6
RNA-seq for DE analysis: the biology behind observed changes - part 6
 
Functional And Pathway Analysis 2010
Functional And Pathway Analysis 2010Functional And Pathway Analysis 2010
Functional And Pathway Analysis 2010
 
RNA-seq for DE analysis: detecting differential expression - part 5
RNA-seq for DE analysis: detecting differential expression - part 5RNA-seq for DE analysis: detecting differential expression - part 5
RNA-seq for DE analysis: detecting differential expression - part 5
 

Similar to Understanding the reference assembly: CSHL Hackathon

Using the GRCh38 reference assembly for clinical interpretation in VSClinical
 Using the GRCh38 reference assembly for clinical interpretation in VSClinical Using the GRCh38 reference assembly for clinical interpretation in VSClinical
Using the GRCh38 reference assembly for clinical interpretation in VSClinical
Golden Helix
 
Advancements in the human genome reference assembly (GRCh38)
Advancements in the human genome reference assembly (GRCh38)Advancements in the human genome reference assembly (GRCh38)
Advancements in the human genome reference assembly (GRCh38)
Genome Reference Consortium
 
Implementation of DNA sequence alignment algorithms using Fpga ,ML,and CNN
Implementation of DNA sequence alignment algorithms  using Fpga ,ML,and CNNImplementation of DNA sequence alignment algorithms  using Fpga ,ML,and CNN
Implementation of DNA sequence alignment algorithms using Fpga ,ML,and CNN
Amr Rashed
 
Visual Exploration of Clinical and Genomic Data for Patient Stratification
Visual Exploration of Clinical and Genomic Data for Patient StratificationVisual Exploration of Clinical and Genomic Data for Patient Stratification
Visual Exploration of Clinical and Genomic Data for Patient Stratification
Nils Gehlenborg
 
Matrix Factorizations at Scale: a Comparison of Scientific Data Analytics on ...
Matrix Factorizations at Scale: a Comparison of Scientific Data Analytics on ...Matrix Factorizations at Scale: a Comparison of Scientific Data Analytics on ...
Matrix Factorizations at Scale: a Comparison of Scientific Data Analytics on ...
Databricks
 
Review of Liao et al - A draft human pangenome reference - Nature (2023)
Review of Liao et al - A draft human pangenome reference - Nature (2023)Review of Liao et al - A draft human pangenome reference - Nature (2023)
Review of Liao et al - A draft human pangenome reference - Nature (2023)
Stuart MacGowan
 
HUG @ NGCLE@e-Novia 15.11.2017
HUG @ NGCLE@e-Novia 15.11.2017HUG @ NGCLE@e-Novia 15.11.2017
HUG @ NGCLE@e-Novia 15.11.2017
NECST Lab @ Politecnico di Milano
 
Integration of single molecule, genome mapping data in a web-based genome bro...
Integration of single molecule, genome mapping data in a web-based genome bro...Integration of single molecule, genome mapping data in a web-based genome bro...
Integration of single molecule, genome mapping data in a web-based genome bro...
William Chow
 
Schneider grc workshop_final
Schneider grc workshop_finalSchneider grc workshop_final
Schneider grc workshop_final
Genome Reference Consortium
 
GIAB Sep2016 Lightning chen sun varmatch
GIAB Sep2016 Lightning chen sun varmatchGIAB Sep2016 Lightning chen sun varmatch
GIAB Sep2016 Lightning chen sun varmatch
GenomeInABottle
 
Processing Terabyte-Scale Genomics Datasets with ADAM: Spark Summit East talk...
Processing Terabyte-Scale Genomics Datasets with ADAM: Spark Summit East talk...Processing Terabyte-Scale Genomics Datasets with ADAM: Spark Summit East talk...
Processing Terabyte-Scale Genomics Datasets with ADAM: Spark Summit East talk...
Spark Summit
 
Folker Meyer: Metagenomic Data Annotation
Folker Meyer: Metagenomic Data AnnotationFolker Meyer: Metagenomic Data Annotation
Folker Meyer: Metagenomic Data Annotation
GigaScience, BGI Hong Kong
 
GIAB Technical Germline Benchmark roadmap discussion
GIAB Technical Germline Benchmark roadmap discussionGIAB Technical Germline Benchmark roadmap discussion
GIAB Technical Germline Benchmark roadmap discussion
GenomeInABottle
 
GIAB for AMP GeT-RM Forum
GIAB for AMP GeT-RM ForumGIAB for AMP GeT-RM Forum
GIAB for AMP GeT-RM Forum
GenomeInABottle
 
GIAB-GRC workshop oct2015 giab introduction 151005
GIAB-GRC workshop oct2015 giab introduction 151005GIAB-GRC workshop oct2015 giab introduction 151005
GIAB-GRC workshop oct2015 giab introduction 151005
GenomeInABottle
 
Rise of AI/ML applications on the National Research Platform
Rise of AI/ML applications on the National Research PlatformRise of AI/ML applications on the National Research Platform
Rise of AI/ML applications on the National Research Platform
Larry Smarr
 
Building bioinformatics resources for the global community
Building bioinformatics resources for the global communityBuilding bioinformatics resources for the global community
Building bioinformatics resources for the global community
ExternalEvents
 
2015 osu-metagenome
2015 osu-metagenome2015 osu-metagenome
2015 osu-metagenome
c.titus.brown
 
Church_GenomeAccess_2013_genome2013
Church_GenomeAccess_2013_genome2013Church_GenomeAccess_2013_genome2013
Church_GenomeAccess_2013_genome2013
Deanna Church
 
Benchmarking with GIAB 220907
Benchmarking with GIAB 220907Benchmarking with GIAB 220907
Benchmarking with GIAB 220907
GenomeInABottle
 

Similar to Understanding the reference assembly: CSHL Hackathon (20)

Using the GRCh38 reference assembly for clinical interpretation in VSClinical
 Using the GRCh38 reference assembly for clinical interpretation in VSClinical Using the GRCh38 reference assembly for clinical interpretation in VSClinical
Using the GRCh38 reference assembly for clinical interpretation in VSClinical
 
Advancements in the human genome reference assembly (GRCh38)
Advancements in the human genome reference assembly (GRCh38)Advancements in the human genome reference assembly (GRCh38)
Advancements in the human genome reference assembly (GRCh38)
 
Implementation of DNA sequence alignment algorithms using Fpga ,ML,and CNN
Implementation of DNA sequence alignment algorithms  using Fpga ,ML,and CNNImplementation of DNA sequence alignment algorithms  using Fpga ,ML,and CNN
Implementation of DNA sequence alignment algorithms using Fpga ,ML,and CNN
 
Visual Exploration of Clinical and Genomic Data for Patient Stratification
Visual Exploration of Clinical and Genomic Data for Patient StratificationVisual Exploration of Clinical and Genomic Data for Patient Stratification
Visual Exploration of Clinical and Genomic Data for Patient Stratification
 
Matrix Factorizations at Scale: a Comparison of Scientific Data Analytics on ...
Matrix Factorizations at Scale: a Comparison of Scientific Data Analytics on ...Matrix Factorizations at Scale: a Comparison of Scientific Data Analytics on ...
Matrix Factorizations at Scale: a Comparison of Scientific Data Analytics on ...
 
Review of Liao et al - A draft human pangenome reference - Nature (2023)
Review of Liao et al - A draft human pangenome reference - Nature (2023)Review of Liao et al - A draft human pangenome reference - Nature (2023)
Review of Liao et al - A draft human pangenome reference - Nature (2023)
 
HUG @ NGCLE@e-Novia 15.11.2017
HUG @ NGCLE@e-Novia 15.11.2017HUG @ NGCLE@e-Novia 15.11.2017
HUG @ NGCLE@e-Novia 15.11.2017
 
Integration of single molecule, genome mapping data in a web-based genome bro...
Integration of single molecule, genome mapping data in a web-based genome bro...Integration of single molecule, genome mapping data in a web-based genome bro...
Integration of single molecule, genome mapping data in a web-based genome bro...
 
Schneider grc workshop_final
Schneider grc workshop_finalSchneider grc workshop_final
Schneider grc workshop_final
 
GIAB Sep2016 Lightning chen sun varmatch
GIAB Sep2016 Lightning chen sun varmatchGIAB Sep2016 Lightning chen sun varmatch
GIAB Sep2016 Lightning chen sun varmatch
 
Processing Terabyte-Scale Genomics Datasets with ADAM: Spark Summit East talk...
Processing Terabyte-Scale Genomics Datasets with ADAM: Spark Summit East talk...Processing Terabyte-Scale Genomics Datasets with ADAM: Spark Summit East talk...
Processing Terabyte-Scale Genomics Datasets with ADAM: Spark Summit East talk...
 
Folker Meyer: Metagenomic Data Annotation
Folker Meyer: Metagenomic Data AnnotationFolker Meyer: Metagenomic Data Annotation
Folker Meyer: Metagenomic Data Annotation
 
GIAB Technical Germline Benchmark roadmap discussion
GIAB Technical Germline Benchmark roadmap discussionGIAB Technical Germline Benchmark roadmap discussion
GIAB Technical Germline Benchmark roadmap discussion
 
GIAB for AMP GeT-RM Forum
GIAB for AMP GeT-RM ForumGIAB for AMP GeT-RM Forum
GIAB for AMP GeT-RM Forum
 
GIAB-GRC workshop oct2015 giab introduction 151005
GIAB-GRC workshop oct2015 giab introduction 151005GIAB-GRC workshop oct2015 giab introduction 151005
GIAB-GRC workshop oct2015 giab introduction 151005
 
Rise of AI/ML applications on the National Research Platform
Rise of AI/ML applications on the National Research PlatformRise of AI/ML applications on the National Research Platform
Rise of AI/ML applications on the National Research Platform
 
Building bioinformatics resources for the global community
Building bioinformatics resources for the global communityBuilding bioinformatics resources for the global community
Building bioinformatics resources for the global community
 
2015 osu-metagenome
2015 osu-metagenome2015 osu-metagenome
2015 osu-metagenome
 
Church_GenomeAccess_2013_genome2013
Church_GenomeAccess_2013_genome2013Church_GenomeAccess_2013_genome2013
Church_GenomeAccess_2013_genome2013
 
Benchmarking with GIAB 220907
Benchmarking with GIAB 220907Benchmarking with GIAB 220907
Benchmarking with GIAB 220907
 

More from Genome Reference Consortium

What's new and what's next for the human reference assembly?
What's new and what's next for the human reference assembly?What's new and what's next for the human reference assembly?
What's new and what's next for the human reference assembly?
Genome Reference Consortium
 
Telomere-to-telomere assembly of a complete human chromosomes
Telomere-to-telomere assembly of a complete human chromosomesTelomere-to-telomere assembly of a complete human chromosomes
Telomere-to-telomere assembly of a complete human chromosomes
Genome Reference Consortium
 
Genome variation graphs with the vg toolkit
Genome variation graphs with the vg toolkitGenome variation graphs with the vg toolkit
Genome variation graphs with the vg toolkit
Genome Reference Consortium
 
The Matched Annotation from NCBI and EMBL-EBI (MANE) Project
The Matched Annotation from NCBI and EMBL-EBI (MANE) ProjectThe Matched Annotation from NCBI and EMBL-EBI (MANE) Project
The Matched Annotation from NCBI and EMBL-EBI (MANE) Project
Genome Reference Consortium
 
Why graph genome storage and updating wakes me up at 4 am
Why graph genome storage and updating wakes me up at 4 amWhy graph genome storage and updating wakes me up at 4 am
Why graph genome storage and updating wakes me up at 4 am
Genome Reference Consortium
 
Mane v2 final
Mane v2 finalMane v2 final
Lrg and mane 16 oct 2018
Lrg and mane   16 oct 2018Lrg and mane   16 oct 2018
Lrg and mane 16 oct 2018
Genome Reference Consortium
 
20181016 grc presentation-pa
20181016 grc presentation-pa20181016 grc presentation-pa
20181016 grc presentation-pa
Genome Reference Consortium
 
2018 1016 trio_binning_ashg_arhie_final
2018 1016 trio_binning_ashg_arhie_final2018 1016 trio_binning_ashg_arhie_final
2018 1016 trio_binning_ashg_arhie_final
Genome Reference Consortium
 
Ashg sedlazeck grc_share
Ashg sedlazeck grc_shareAshg sedlazeck grc_share
Ashg sedlazeck grc_share
Genome Reference Consortium
 
171017 giab for giab grc workshop
171017 giab for giab grc workshop171017 giab for giab grc workshop
171017 giab for giab grc workshop
Genome Reference Consortium
 
101717.kh miga ashg_grc
101717.kh miga ashg_grc101717.kh miga ashg_grc
101717.kh miga ashg_grc
Genome Reference Consortium
 

More from Genome Reference Consortium (12)

What's new and what's next for the human reference assembly?
What's new and what's next for the human reference assembly?What's new and what's next for the human reference assembly?
What's new and what's next for the human reference assembly?
 
Telomere-to-telomere assembly of a complete human chromosomes
Telomere-to-telomere assembly of a complete human chromosomesTelomere-to-telomere assembly of a complete human chromosomes
Telomere-to-telomere assembly of a complete human chromosomes
 
Genome variation graphs with the vg toolkit
Genome variation graphs with the vg toolkitGenome variation graphs with the vg toolkit
Genome variation graphs with the vg toolkit
 
The Matched Annotation from NCBI and EMBL-EBI (MANE) Project
The Matched Annotation from NCBI and EMBL-EBI (MANE) ProjectThe Matched Annotation from NCBI and EMBL-EBI (MANE) Project
The Matched Annotation from NCBI and EMBL-EBI (MANE) Project
 
Why graph genome storage and updating wakes me up at 4 am
Why graph genome storage and updating wakes me up at 4 amWhy graph genome storage and updating wakes me up at 4 am
Why graph genome storage and updating wakes me up at 4 am
 
Mane v2 final
Mane v2 finalMane v2 final
Mane v2 final
 
Lrg and mane 16 oct 2018
Lrg and mane   16 oct 2018Lrg and mane   16 oct 2018
Lrg and mane 16 oct 2018
 
20181016 grc presentation-pa
20181016 grc presentation-pa20181016 grc presentation-pa
20181016 grc presentation-pa
 
2018 1016 trio_binning_ashg_arhie_final
2018 1016 trio_binning_ashg_arhie_final2018 1016 trio_binning_ashg_arhie_final
2018 1016 trio_binning_ashg_arhie_final
 
Ashg sedlazeck grc_share
Ashg sedlazeck grc_shareAshg sedlazeck grc_share
Ashg sedlazeck grc_share
 
171017 giab for giab grc workshop
171017 giab for giab grc workshop171017 giab for giab grc workshop
171017 giab for giab grc workshop
 
101717.kh miga ashg_grc
101717.kh miga ashg_grc101717.kh miga ashg_grc
101717.kh miga ashg_grc
 

Recently uploaded

Active and Passive Surveillance of pharmacovigillance
Active and Passive Surveillance of pharmacovigillanceActive and Passive Surveillance of pharmacovigillance
Active and Passive Surveillance of pharmacovigillance
SejalAgrawal43
 
Science-Technology Quiz (School Quiz 2024)
Science-Technology Quiz (School Quiz 2024)Science-Technology Quiz (School Quiz 2024)
Science-Technology Quiz (School Quiz 2024)
Kashyap J
 
Testing the Son of God Hypothesis (Jesus Christ)
Testing the Son of God Hypothesis (Jesus Christ)Testing the Son of God Hypothesis (Jesus Christ)
Testing the Son of God Hypothesis (Jesus Christ)
Robert Luk
 
GIT hormones- II_12345677809876543235780963.pptx
GIT hormones- II_12345677809876543235780963.pptxGIT hormones- II_12345677809876543235780963.pptx
GIT hormones- II_12345677809876543235780963.pptx
muralinath2
 
Dalghren, Thorne and Stebbins System of Classification of Angiosperms
Dalghren, Thorne and Stebbins System of Classification of AngiospermsDalghren, Thorne and Stebbins System of Classification of Angiosperms
Dalghren, Thorne and Stebbins System of Classification of Angiosperms
Gurjant Singh
 
El Nuevo Cohete Ariane de la Agencia Espacial Europea-6_Media-Kit_english.pdf
El Nuevo Cohete Ariane de la Agencia Espacial Europea-6_Media-Kit_english.pdfEl Nuevo Cohete Ariane de la Agencia Espacial Europea-6_Media-Kit_english.pdf
El Nuevo Cohete Ariane de la Agencia Espacial Europea-6_Media-Kit_english.pdf
Champs Elysee Roldan
 
Modelling, Simulation, and Computer-aided Design in Computational, Evolutiona...
Modelling, Simulation, and Computer-aided Design in Computational, Evolutiona...Modelling, Simulation, and Computer-aided Design in Computational, Evolutiona...
Modelling, Simulation, and Computer-aided Design in Computational, Evolutiona...
University of Maribor
 
Detection of the elusive dangling OH ice features at ~2.7 μm in Chamaeleon I ...
Detection of the elusive dangling OH ice features at ~2.7 μm in Chamaeleon I ...Detection of the elusive dangling OH ice features at ~2.7 μm in Chamaeleon I ...
Detection of the elusive dangling OH ice features at ~2.7 μm in Chamaeleon I ...
Sérgio Sacani
 
Bragg Brentano Alignment for D4 with LynxEye Rev3.pptx
Bragg Brentano Alignment for D4 with LynxEye Rev3.pptxBragg Brentano Alignment for D4 with LynxEye Rev3.pptx
Bragg Brentano Alignment for D4 with LynxEye Rev3.pptx
Lisandro Cunci
 
BIOPHYSICS Interactions of molecules in 3-D space-determining binding and.pptx
BIOPHYSICS Interactions of molecules in 3-D space-determining binding and.pptxBIOPHYSICS Interactions of molecules in 3-D space-determining binding and.pptx
BIOPHYSICS Interactions of molecules in 3-D space-determining binding and.pptx
alishyt102010
 
poikilocytosis 23765437865210857453257844.pptx
poikilocytosis 23765437865210857453257844.pptxpoikilocytosis 23765437865210857453257844.pptx
poikilocytosis 23765437865210857453257844.pptx
muralinath2
 
Gasification and Pyrolyssis of plastic Waste under a Circular Economy perpective
Gasification and Pyrolyssis of plastic Waste under a Circular Economy perpectiveGasification and Pyrolyssis of plastic Waste under a Circular Economy perpective
Gasification and Pyrolyssis of plastic Waste under a Circular Economy perpective
Recupera
 
Liver & Gall Bladder 23098463278654387654328765439875.pptx
Liver & Gall Bladder 23098463278654387654328765439875.pptxLiver & Gall Bladder 23098463278654387654328765439875.pptx
Liver & Gall Bladder 23098463278654387654328765439875.pptx
muralinath2
 
Possible Anthropogenic Contributions to the LAMP-observed Surficial Icy Regol...
Possible Anthropogenic Contributions to the LAMP-observed Surficial Icy Regol...Possible Anthropogenic Contributions to the LAMP-observed Surficial Icy Regol...
Possible Anthropogenic Contributions to the LAMP-observed Surficial Icy Regol...
Sérgio Sacani
 
Probing the northern Kaapvaal craton root with mantle-derived xenocrysts from...
Probing the northern Kaapvaal craton root with mantle-derived xenocrysts from...Probing the northern Kaapvaal craton root with mantle-derived xenocrysts from...
Probing the northern Kaapvaal craton root with mantle-derived xenocrysts from...
James AH Campbell
 
Collaborative Team Recommendation for Skilled Users: Objectives, Techniques, ...
Collaborative Team Recommendation for Skilled Users: Objectives, Techniques, ...Collaborative Team Recommendation for Skilled Users: Objectives, Techniques, ...
Collaborative Team Recommendation for Skilled Users: Objectives, Techniques, ...
Hossein Fani
 
2. Osmotic pressure, osmotic potential, turgor pressure, wall pressure, water...
2. Osmotic pressure, osmotic potential, turgor pressure, wall pressure, water...2. Osmotic pressure, osmotic potential, turgor pressure, wall pressure, water...
2. Osmotic pressure, osmotic potential, turgor pressure, wall pressure, water...
khadija07kubra
 
ANTIGENS_.pptx ( Ranjitha SL) PRESENTATION SLIDE
ANTIGENS_.pptx ( Ranjitha SL) PRESENTATION SLIDEANTIGENS_.pptx ( Ranjitha SL) PRESENTATION SLIDE
ANTIGENS_.pptx ( Ranjitha SL) PRESENTATION SLIDE
RanjithaSL
 
Forces grade 9 slideshow used for grade 9
Forces grade 9 slideshow used for grade 9Forces grade 9 slideshow used for grade 9
Forces grade 9 slideshow used for grade 9
manavhelamuki
 
LOB LOD LOQ for method validation in laboratory
LOB LOD LOQ for method validation in laboratoryLOB LOD LOQ for method validation in laboratory
LOB LOD LOQ for method validation in laboratory
JCKH
 

Recently uploaded (20)

Active and Passive Surveillance of pharmacovigillance
Active and Passive Surveillance of pharmacovigillanceActive and Passive Surveillance of pharmacovigillance
Active and Passive Surveillance of pharmacovigillance
 
Science-Technology Quiz (School Quiz 2024)
Science-Technology Quiz (School Quiz 2024)Science-Technology Quiz (School Quiz 2024)
Science-Technology Quiz (School Quiz 2024)
 
Testing the Son of God Hypothesis (Jesus Christ)
Testing the Son of God Hypothesis (Jesus Christ)Testing the Son of God Hypothesis (Jesus Christ)
Testing the Son of God Hypothesis (Jesus Christ)
 
GIT hormones- II_12345677809876543235780963.pptx
GIT hormones- II_12345677809876543235780963.pptxGIT hormones- II_12345677809876543235780963.pptx
GIT hormones- II_12345677809876543235780963.pptx
 
Dalghren, Thorne and Stebbins System of Classification of Angiosperms
Dalghren, Thorne and Stebbins System of Classification of AngiospermsDalghren, Thorne and Stebbins System of Classification of Angiosperms
Dalghren, Thorne and Stebbins System of Classification of Angiosperms
 
El Nuevo Cohete Ariane de la Agencia Espacial Europea-6_Media-Kit_english.pdf
El Nuevo Cohete Ariane de la Agencia Espacial Europea-6_Media-Kit_english.pdfEl Nuevo Cohete Ariane de la Agencia Espacial Europea-6_Media-Kit_english.pdf
El Nuevo Cohete Ariane de la Agencia Espacial Europea-6_Media-Kit_english.pdf
 
Modelling, Simulation, and Computer-aided Design in Computational, Evolutiona...
Modelling, Simulation, and Computer-aided Design in Computational, Evolutiona...Modelling, Simulation, and Computer-aided Design in Computational, Evolutiona...
Modelling, Simulation, and Computer-aided Design in Computational, Evolutiona...
 
Detection of the elusive dangling OH ice features at ~2.7 μm in Chamaeleon I ...
Detection of the elusive dangling OH ice features at ~2.7 μm in Chamaeleon I ...Detection of the elusive dangling OH ice features at ~2.7 μm in Chamaeleon I ...
Detection of the elusive dangling OH ice features at ~2.7 μm in Chamaeleon I ...
 
Bragg Brentano Alignment for D4 with LynxEye Rev3.pptx
Bragg Brentano Alignment for D4 with LynxEye Rev3.pptxBragg Brentano Alignment for D4 with LynxEye Rev3.pptx
Bragg Brentano Alignment for D4 with LynxEye Rev3.pptx
 
BIOPHYSICS Interactions of molecules in 3-D space-determining binding and.pptx
BIOPHYSICS Interactions of molecules in 3-D space-determining binding and.pptxBIOPHYSICS Interactions of molecules in 3-D space-determining binding and.pptx
BIOPHYSICS Interactions of molecules in 3-D space-determining binding and.pptx
 
poikilocytosis 23765437865210857453257844.pptx
poikilocytosis 23765437865210857453257844.pptxpoikilocytosis 23765437865210857453257844.pptx
poikilocytosis 23765437865210857453257844.pptx
 
Gasification and Pyrolyssis of plastic Waste under a Circular Economy perpective
Gasification and Pyrolyssis of plastic Waste under a Circular Economy perpectiveGasification and Pyrolyssis of plastic Waste under a Circular Economy perpective
Gasification and Pyrolyssis of plastic Waste under a Circular Economy perpective
 
Liver & Gall Bladder 23098463278654387654328765439875.pptx
Liver & Gall Bladder 23098463278654387654328765439875.pptxLiver & Gall Bladder 23098463278654387654328765439875.pptx
Liver & Gall Bladder 23098463278654387654328765439875.pptx
 
Possible Anthropogenic Contributions to the LAMP-observed Surficial Icy Regol...
Possible Anthropogenic Contributions to the LAMP-observed Surficial Icy Regol...Possible Anthropogenic Contributions to the LAMP-observed Surficial Icy Regol...
Possible Anthropogenic Contributions to the LAMP-observed Surficial Icy Regol...
 
Probing the northern Kaapvaal craton root with mantle-derived xenocrysts from...
Probing the northern Kaapvaal craton root with mantle-derived xenocrysts from...Probing the northern Kaapvaal craton root with mantle-derived xenocrysts from...
Probing the northern Kaapvaal craton root with mantle-derived xenocrysts from...
 
Collaborative Team Recommendation for Skilled Users: Objectives, Techniques, ...
Collaborative Team Recommendation for Skilled Users: Objectives, Techniques, ...Collaborative Team Recommendation for Skilled Users: Objectives, Techniques, ...
Collaborative Team Recommendation for Skilled Users: Objectives, Techniques, ...
 
2. Osmotic pressure, osmotic potential, turgor pressure, wall pressure, water...
2. Osmotic pressure, osmotic potential, turgor pressure, wall pressure, water...2. Osmotic pressure, osmotic potential, turgor pressure, wall pressure, water...
2. Osmotic pressure, osmotic potential, turgor pressure, wall pressure, water...
 
ANTIGENS_.pptx ( Ranjitha SL) PRESENTATION SLIDE
ANTIGENS_.pptx ( Ranjitha SL) PRESENTATION SLIDEANTIGENS_.pptx ( Ranjitha SL) PRESENTATION SLIDE
ANTIGENS_.pptx ( Ranjitha SL) PRESENTATION SLIDE
 
Forces grade 9 slideshow used for grade 9
Forces grade 9 slideshow used for grade 9Forces grade 9 slideshow used for grade 9
Forces grade 9 slideshow used for grade 9
 
LOB LOD LOQ for method validation in laboratory
LOB LOD LOQ for method validation in laboratoryLOB LOD LOQ for method validation in laboratory
LOB LOD LOQ for method validation in laboratory
 

Understanding the reference assembly: CSHL Hackathon