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Introduction to gEVAL

This is a quick tutorial of the genome evaluation browser, gEVAL. Please visit http://geval.sanger.ac.uk for more details

William Chow

on 11 August 2017

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Transcript of Introduction to gEVAL

..Most likely the first page that pops up after using the landing pages to choose a specific region is this "Region in Detail" browsable window.
Introduction to
A Genome Evaluation Browser
Portal to Punchlists (more about this later)
Clicking on an Assembly...
...Returns the assembly landing page
You can quickly access a region of interest either through..
Here or...
Karyotype Page
Primary Components are drawn out, like
Other top-level components are in pull-down menu
such as unlocalized scaffolds.
Getting to the assembly you want
Clicking on the image or the drop down menu will bring you to a specific region for in-depth investigation.
Lets look at the Navigation tabs
Chromosome Summary
Like the Karyotype, but specfically for the
individual chromosome/object currently
the browser is on. Includes simple statistics
for the component.
Marker Overview
Currently only available for zebrafish
assemblies. Returns aggregated
marker median positions and upper
lower deciles for the SATMap Panel.
Intra-species Comparisons
gEVAL Compara opens up a view for comparing alignments between assemblies that exist in the viewer
Data Control
Ability to add data such as GFF, dump the sequence in fasta format to your web browser or a text file for the region you are viewing or provide appropriate links.
The "meat and potatoes" of the site
Region navigation can be controlled here
Search region or sequence id. Region should follow format X:start-end, for example 8:100-1000
Zoom in and out and
move up/downstream in
increments here
Zoom out directly to 2Mb
window here
Lets look at this Region in Detail page at bit more....
There are 3 viewing windows at different scales
Chromosome Overview: your region (red box) relative to the top-level component
Detailed View (Top Window): A more zoomed in with tracks showing the components on the path. Markers can be turned on in this window
Detailed View (Bottom Window): The region of interest. Here is where all the tracks of data can be turned on and interrogated. This is the most detailed browsing window available.
Each window can be configured, shared, and image exported
Switch for genoverse scrolling or static browsing
Data in all window can be clicked to reveal additional information. Dragging will return a box to isolate new region of interest.
Again the Region in Detail Page only returns a maximum 2Mb window. For a larger window, use Region Overview...
Region Overview
Region overview expands on the 2Mb window limit allowing the visualization of the entire toplevel component or chromosome. The only limitation is this view lacks the number of data/analysis tracks as compared to region in detail. Above is a 10Mb window.
Region in Detail
TPF View
This returns the ordered components (the tile path) used in the assembly. This provides faster access and a larger snapshot of the path compared to a visual representation. Useful additional information include:
Tables in gEVAL allows text-based filtering of results, just type a few letters,and results filter on the fly.
Marker List
A table listing the markers in the region, where its mapped on the assembly, the components, and where it is expected to be mapped and the approx map distance.
(25)mp:71.022 => map info puts this marker on chr 25 with mp 71.022, not on the current assembly position of chr 5
These set of markers here indicate map placement on chr 5 and a clear descending order of mp, indicating correct placement of components on the assembly.
Data and Analysis mappings
Tracks represent a row presenting a set of data in the browser. This row contains glyphs of data that can be clicked on for further information via a popup menu
Clone End Mappings
cDNA/Transcript Mappings
Self Comparisons
Component Placements & orientation can be aided using by the color coded marker track.
Component Overlap
The components overlapping join that are used to build the assembly/tile path can be visualized, including the amount of variation in the overlap region.
Tutorial takes approximately 15mins
Different species and assemblies may have unique tracks specific to the project. Below are the most common tracks available.
Questions, Comments?
Whole Genome
Returns to the Karyotype Page
Component Stats
Statistics of components such as clones organized per toplevel components such as chromosomes
Chromosome Summary
Like the karyotype page, but specifically for the individual chromosome/object currently the browser is on. Includes statistics for the chromosome.
TPF View
List of components involved in the region as viewed like a tilepath
Marker Overview
This is currently only available for zebrafish. It returns SATMap marker aggregates and the lower/upper deciles of map positions in the region.
Region Overview
The Broadest view. Here the chromosome can be viewed at no size limits. However because of this only a limited number of tracks are available, and this varies with each organism. Examples include JIRA tickets, fpc contigs and clones.
Region in Detail
The primary view. Currently a max limit of 2Mb size viewable window is allowed. Here is where you can turn on all the tracks via the configure page on the left navigation bar.
Comparative Genomics
gEVAL Compara, Intra-species alignments. This page allows the user to compare assemblies in a given species.
returns all mapped markers in the region that is being viewed, and links to the appropriate marker information
Configure this Page
Use this tab to configure tracks on the browser. You can also use this to configure the look of the browser, such as increasing the viewable size of the browser window.
Data Control
Ability to add data such as GFF, dump the sequence in FASTA format to your web browser or a text file for the region you are viewing or share a link with the exact region configurations you are viewing.
Clone end libraries are mapped and color coded for concordance.
Selfcomp alignments may provide information on regions of assembly overexpansion and misplacements.
Mappings indicate potential overlap of adjacent components. Further investigations may yield unnecessary insertion of gap.

Correct Chr 12 Placement
Incorrect Placement (Chr 5)
A detailed table representation is also available, and can be exported out as a file.
Navigation to previous/next low quality overlap can also be made directly from the menu of the feature.
Other Analyses
Lists, comparative genomics & other data
Punchlists are automatically generated lists of regions of interests or of problematic areas that need to be resolved.
Example list of high variation overlaps, sorted by Chromosome & region start/end.
If there is a punchlist you would like added to an assembly, please get in touch with us.
Comparative Genomics
Optical & Genome Maps
Optical and Genome Maps are in a way similar to large physical maps with applications such as assembly scaffolding, correction and SV identification. gEVAL hosts maps from commercial technologies:
Bionano Genomics
, as well as data produced from
David Schwartz's lab at the University of Wisconsin
. Click below for an overview of the Bionano technology:
Example of Usage

Insilico Digest Of the Genome
(Bspq1 nickase)
Bionano Genome Map
By comparing the fragment sizes between cut/nick labels of the genome map against the insilico digest map of the genome assembly, regions of discordance can be found and further evaluated.
In the genome map, the
red fragments
are regions of discordance against the
insilico digest
There is a discrepancy in sizes.
Insilico digest
- 11.568 kb
Genome Map
- over 20 kb
This difference is most likely caused by missing sequence within the assembly as highlighed by the 4 gaps between components.
More Genome Map Examples
Including ...
Example 1: Gap Sizing:
Example 2: Confirmation of Assembly Components:
Example 3: Issue Detection in Components:
Example 4: Missing sequence affecting Relevant Human Gene
Example 5: Over-expansion in Assemblies
Example 6: SV representation and Mendelian inheritance patterns in Human Trio
The button will then bring up a pop up window where one can choose the assemblies to compare with
After selection of species, the page will reload with the comparative alignment view between selected assemblies against the query genome.
Missing Sequence in Query Assembly appears in both selected Assemblies
Potential inverted Duplication
Need More Help & Info
Green mappings - over 98% coverage of transcript
Orange mappings - under 98% coverage of transcript
Color coding of incomplete transcript mappings will indicate whether the region has an issue.
There is also Genome maps (covered in later topic) indicating there is some sort of fragment size variation (red bit) in the middle of the incomplete transcript which appears to be the root of the issue.
Best Viewed
in Full Screen
This is the gEVAL landing page where you can
choose the species/assembly of interest.
Under each species page lists the different assemblies available
Landing Pages
gEVAL Interim Releases: Produced
by the Genome Reference Informatics Team
gEVAL Builds based on major public
gEVAL Builds based on other public assemblies:
such as WGS or hybrid Next-Gen Releases
GRC region-specific assembly releases:
By User Requests
One can quickly prioritize by sorting and even export the results, or quickly navigate to a detailed region view of the issue.
Clicking the Comparative Genomics/Analysis tab
will activate the "Select species" to appear.
Indels, Variation and missing sequence can be observed.
News and Announcements
Updated Jan 2016
Image Credits: NBBJ Architects
(Wellcome Trust Sanger Institute)

gEVAL is managed by the Genome Reference Informatics team at the Wellcome Trust Sanger Institute ( http://bit.ly/1Kh6WO0 )
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