The gEVAL Browser, based on the Ensembl project, produces genome databases, for assisting in sequencing vertebrates and other eukaryotic species. Genome Reference Informatics - Wellcome Trust Sanger Institute.

1. gEVAL – A Genome Evaluation Browser for Improving Genome Assemblies!
William Chow, Kim Brugger, Britt Kilian, James Torrance, Eduard Zuiderwijk, and Kerstin Howe!
Wellcome Trust Sanger Institute, Cambridge, UK.!
http://geval.sanger.ac.uk!
geval-help@sanger.ac.uk!
gEVAL Punchlists and Issue Navigation!
Automated lists created to facilitate identification of and navigation to issues or regions of
interest. In browser menus also help to jump between issues.!
!
Optical Maps!
Optical map data are ordered restriction maps from single stained molecules of DNA that can be
aligned against assemblies. gEVAL hosts some of this data for human and mouse and aids in
identifying genomic regions that requires attention, such as rearrangements or mis-representation
of sequence and haplotypes. !
!
Introduction!
The web-accessible 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. This facilitates the improvement of overall
assemblies to a “gold” standard for release as reference genomes.!
Mapped multiple times
Wrong direction (<<, <>, >>)
Wrong distance from partner
Integration of GRC Review/Status Update System!
A! s part of the GRC curation process,
regions of interest that are to be
evaluated are tagged and tracked via
the GRC review ticketing system. !
!
Both resolved and unresolved tickets are
visible for viewing as a track on the
browser or as a dedicated punchlist. !
!
A summary of the features in the region
associated with the ticket is also available
(right insert).!
Visual Representation of Current Assembly State!
Our build cycle is frequent, and thus can represent a current snapshot of the
assembly. As we are part of the GRC, we also have first access to major GRC
assembly releases.!
Component
in
sequencing
Pipeline.
Phase
1
unfinished
component.
Phase
2/3
finished
component.
Comparative Genomics!
gEVAL includes comparative analyses of different assembly builds for each species. This
helps in identifying missing sequences, reference assembly errors and haplotypic variation.!
!
A gap separates two clone
components in a zebrafish
bulid. Investigating the
alignments against two whole
genome shotgun (wgs)
assemblies reveal size of gap
and missing sequence.!
A region of the wgs is used to
cover the gap in a later build.
(bonus: a clone is also in
pipeline, grey box above). !
The clone component AL596089
contains a deletion and is
highlighted by the 3 cell line optical
map analysis (right). This would not
have been captured because the
clone overlaps do not extend far
enough to show this. An issue that
is tagged and reported in GRC
ticket: HG-1482.!
!
Optical Map data provided by the D.
Schwartz Lab (UW Madison).!
Popup menus on tracks to quickly
help navigate between previous/
next overlap between components
along a chr (below).!
An example overview of punchlists available. Punchlists can be
tailored for different projects, on request (above).!
Components potentially placed on the wrong chr using marker
evidence listed per chr (below).!
Current Species Available!
Identify Problematic/Incomplete Transcript Mappings!
GREEN – 98% cutoff coverage !
ORANGE – Incomplete or problematic transcript!
!
• This example shows how a region of 2
clones (dark/light blue boxes on contig
track) have incorrect orientation.!
• The overlapping gene ryr1b, therefore
looked to be split on opposite strands!
• The incorrect orientation of 2 gap
spanning fosmids confirmed the
assertion that CU138549 was in the
wrong orientation.!
!
The up to date path returns the correct
gene structure and clone end mapping.!
before!
after!
Examine Large Region of Interest!
View region windows of up to 2Mb, allowing for greater vantage of possible
problematic areas. The Region overview page provides a less detailed snapshot
of larger windows up to the entire chromosome or top level component.!
!
!
Region overview can show, for example, the state of the assembly and how much are unfinished,
finished or sequence that is in production. Above is a snapshot of a region just under 10Mb and
the clones in the path. Status of clones can be quickly scanned and regions prioritized. !
Clone End Library Mappings!
!
Mapped 1 time
Spanning partner in the vicinity
Clone end mappings in gEVAL are unique
due to how they are displayed, facilitating
the ease of identifying concurrent clones
or inconsistencies relating to a potential
problem with the assembly. Clones can be
picked to close gap regions or to span
regions of interest for further interrogation.!
!
before!
after!
The above example illustrates using end placements to pick clones to cover gaps. In the before
image, there is a gap with a BAC clone spanning the gapped region according to their end
placements (orange). In the subsequent assembly (after image above) with the clone
sequenced, the unfinished clone places well in the region, as illustrated by the green clone
overlaps.!
Human!
GRCh38, GRCh37pX (latest patch),
NCBI36, CHM1_1.1, NA12878, HuREF,
YH1/2.0. !
Zebrafish!
Zv9, WGS28, WGS29, WGS31, !
z.2013.12.06, z.2014.03.14.!
!
Mouse!
GRCm38, GRCm38pX (latest patch),
GRCm37B/C, NCBIm37, wgs_c57bl6j,
wgs_celera, MGSCv3, m.2013.03.15.!
Helminth!
Echinococcus multilocularis!
Schistosoma mansoni !
Stronglyoides ratti!
Genome Reference Consortium!
The Genome Reference Consortium (GRC) is a partnership between the Sanger Institute,
NCBI, EBI and the Genome Institute at Wash U tasked with improving and providing accurate
reference genomes. This includes releasing the reference assemblies of human, mouse and
zebrafish. !
Pig!
Sscrofa10.2!
The red arrows highlights the
incorrect orientation of these
ryr1b gene split fosmid ends. !
on opposite
strands!
Clone end placements reveal sequence that can be placed in the gap
region. Assembly reveals newly sequenced clone in path.!