1.
gVAL Browser and the GRC TrackHub
Laura Clarke
http://geval.sanger.ac.uk/

2.
• gVAL Browser
• GRC TrackHub
• 1000 Genomes and GRCh38

3.
gEVAL Browser
• Evaluation of Genome Assemblies
• Based on Ensembl Framework
• Run by Sanger Institute
• Navigation of current assemblies
• View different annotation
• Punchlists of Assembly Issues
http://geval.sanger.ac.uk/

4.
gEVAL Browser - Annotation
• Intra species alignments
• Optical Map data
• Clone End mapping
• Black Tags/Clone sequence anomalies
• Self Comparisons
• CCDS Alignments
• RefSeq Alignments
• Repeat Annotation
– Centromeric repeats
– Telomeric repeats
– 1000 Genomes identified Mobile Element Insertions
http://geval.sanger.ac.uk/

5.
Human Build Info
• Primary Reference
– GRCh38
• Current Build
– Human 20140826
• Older Versions
– GRCh37.p13
– NCBI36
• Other Assemblies
– CHM1_1.1
– NA12878
– Huref
– YH2.0
http://geval.sanger.ac.uk/

6.
http://geval.sanger.ac.uk/

7.
Intra-species comparisons

8.
GRCh37 vs HuRef
GRCh38
HuRef
GRCh37
http://geval.sanger.ac.uk/

9.
GRCh38
HuRef
GRCh37
GRCh38 fix.
http://geval.sanger.ac.uk/

10.
HG-1312 (add wgs to PATH)

11.
Add fix to GRCh38
http://geval.sanger.ac.uk/

12.
Clone End Library Mappings
19 Human Clone Libraries
• Reveals state of assembly
• Orientation
• Mis-assemblies
• Incorrect location
• Source of new sequence
Mapped 1 time
Mapped multiple times
Wrong direction (<<, <>, >>)
Wrong distance from partner
Spanning partner in the vicinity
http://geval.sanger.ac.uk/

13.
Clone End Library Mappings

14.
Clone End Library Mappings
http://geval.sanger.ac.uk/

15.
Using Clone End Library Mappings
before
after
http://geval.sanger.ac.uk/

16.
Optical Maps
• ..ordered restriction maps from single stained molecules of
DNA.
• D.Schwartz (UW-Madison)
http://geval.sanger.ac.uk/

17.
TrackHub
http://ngs.sanger.ac.uk/production/grit/track_hub/hub.tx
t
Display GRC issues in Ensembl and UCSC
• Genome issues under review by the GRC
• Genomic regions defined by the GRC
• Alignments between the primary assembly and
alternate loci or patches
• Clone sequence anomalies
• Human regions with clones from the CHORI-17 library
(CHM1tert)

18.
Adding a TrackHub to Ensembl
http://ngs.sanger.ac.uk/production/grit/track_hub/hub.txt

19.
Adding a TrackHub to Ensembl

20.
TrackHub Display 1:12956267-
13431650

21.
Adding a TrackHub to UCSC

22.
Adding a TrackHub to UCSC

23.
TrackHub Display 1:12956267-
13431650

24.
TrackHub Display 1:12956267-
13431650

25.
The 1000 Genomes Project
• IGSR established to maintain 1000 Genomes Data
• Phase 3 release is out on GRCh37
• Reads will be remapping in 1Q 2015
• dbSNP has GRCh38 mapping for most sites now
• Plan to recall/map in 2Q 2015

26.
Acknowledgments
GRIT (Team135)
• Kate Auger
• Joanna Collins
• Guy Griffith
• Glenn Harden
• Paul Heath
• Britt Kilian
• Kerstin Howe
• Sarah Pelan
• Glen Threadgold
• James Torrance
• Jo Wood
Alumni
• Kim Brugger
• Mario Caccamo
• Ian Sealy
• Tina Eyre
• Ed Zuiderwijk
• James Smith
• Paul Bevan
• Simon Brent
• Harpreet Riat
• David Harper
• David Schwartz (UW Madison)
• Steve Goldstein (UWMadison)
• Evan Eichler (Uwashington)
• Jeff Kid (Uwashington)
http://geval.sanger.ac.uk/