Sequence, Finishing and the Future Conference (SFAF 2015) Poster submission. Santa Fe, New Mexico. Poster describes the gEVAL browser, and the integration of genome/optical map data for use in evaluating/curation of genome assemblies. Human, Mouse, Zebrafish, Pig, Helminth, Chicken.

1. Integration of single molecule, genome mapping data in a web-based genome
browser for evaluating sequence based structural artifacts
William Chow, Matthew Dunn, Jonathan Wood and Kerstin Howe
Wellcome Trust Sanger Institute, Cambridge, UK.
Introduction
The publicly available gEVAL browser (http://geval.sanger.ac.uk) allows the evaluation of genome
assemblies through its tools and pre-computed analyses. The strength of this browser is the ability to
navigate an up to date assembly and identify problematic regions and assisting in strategizing potential
solutions for these issues.
To aid in this, we have generated data from single molecule, genome and optical mapping technologies
and have added this to gEVAL. This is the first instance such data has been integrated into a public web-
based genome browser. Along with the wide range of data already aligned to each genome, this long
range data can help identify and confirm assembly irregularities such as insertions, deletions and mis-
assemblies whilst providing suitable information to resolve them.
Current Species Available
http://geval.sanger.ac.uk
Human
• GRCh38 ‡
• GRCh37 †
• NCBI36
• NA12878
• CHM1_1.1
• CHM1tert
• HuREF
• YH1/2.0
• Mongolian
Genome
Zebrafish
• GRCz10
• Zv9
• WGS28
• WGS29
• WGS31
• WGS32
Mouse
• GRCm38 †
• GRCm37B/C
• NCBIm37
• WGS_c57bl6j
• WGS_Celera
• MGSCv3
• CAST_EiJ §
• SPRET_EiJ §
• C57BL_6NJ §
• PWK_PhJ §
Helminth
• Echinococcus multilocularis
• Schistosoma mansoni
• Stronglyoides ratti
geval-help@sanger.ac.uk
Pig
• Sscrofa10.2
Chicken
• Galgal4
• Galgal4.1(PB)
Available Genome/Optical Map Data in gEVAL
Platform Currently Available in gEVAL In the Pipeline
Strain used for map gEVAL DB alignment
Human (CHM1) • CHM1_1.1
• GRCh38
Mouse
• 14 of 18 strains from Mouse Genome Project
will have Bionano maps produced.Zebrafish (SAT F1) • GRCz10
Mouse specific strains • CAST/EiJ
• SPRET/EiJ
Mouse
• 2 of 18 strains from Mouse Genome Project
Zebrafish (SAT F1)Chicken • Galgal4.1(PB)
Data produced by:
Prof. David Schwartz and
Steve Goldstein
Human
• GM10860
• GM15510
• GM18994
• GRCh37
• GRCh38
None
Mouse
• C57BL/6J
• GRCm37
• GRCm38
† - Including Latest Patch Versions
‡ - Including Latest Patch Version & Decoy
§ - an additional 14 mouse strains in pipeline as of print
as part of 18 strains from the Mouse Genome Project
Genome mapping (BioNano, OpGen) & Optical map (D.Schwartz) data are ordered restriction maps from single stained molecules
of DNA that can be aligned against assemblies. gEVAL hosts some of this data for various species and aids in identifying genomic
regions that requires attention, such as rearrangements or mis-representation of sequence and haplotypes
Applications:
• Scaffolding of draft genomes
• Gap Sizing
• Confirmation of components
in tilepath
• Orientation
• Rearrangement
• Structural variation
Gap Sizing
Gaps in an assembly can be accurately sized using genome
maps (see black lines below). This can help in choosing the
appropriate strategy to use for closing this gap.
Identifying discordance between genome map and assembly
The example below illustrates discordance between the fragment alignments from the insilico digest† of the assembly and the Bionano
genome map†. The assembly digest reveals a fragment size of 11568 (purple block), whereas the map reveals additional cutsites creating 4
fragments (red block).
Insilico digest of assembly
Genome map consensus map contig
Structural variation track
† BspQI nickase used.
Structural Variation
The human clone
component AL596089
contains a deletion and
is highlighted by the 3
cell line optical map
analysis created by the
Schwartz group (right).
Scaffolding
Punchlists are also
available to highlight
the potential joins of
assembly components.
Genome Reference Consortium
The authors are affiliated with the Genome Reference Consortium (GRC), a partnership between the Sanger Institute, NCBI, EBI
and the Genome Insititute at WashU tasked with improving and
providing accurate reference genomes.
The gEVAL Browser
For an overview and usage examples of the gEVAL Browser
please take one of the handouts
Example
of
Data
Tracks
in
gEVAL
Clone
Library
Ends
Transcripts/cDNAs
Assembly
Self
Comparisons
GRC
Issue
Tracker
Markers
Highlights
Punchlists
and
Issue
Naviga?on
Automated lists created to facilitate
identification of and navigation to issues
or regions of interest
Compara?ve
Genomics
gEVAL includes comparative analyses of
different assembly builds for each
species.
gEVAL is a modern, scrollable and dynamic genome browser, allowing the user to view pre-calculated analyses or attach data
as tracks specifically tailored for assembly evaluation