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Reference genome assemblies:
Resources & updates from the GRCValerie Schneider, Ph.D.
NCBI16 July 2016
https://genomereference.org
Outline
Outline GRC Introduction Assembly updates Assembly resources
https://genomereference.org
Outline GRC Introduction Assembly updates Assembly resources
https://genomereference.org
Outline
Assembly (e.g. GRCm38)
Primary Assembly
Unit(C57BL/6J)
Non-nuclear assembly unit
(e.g. MT)
129S6/SvEvTac
129S1/SvImJ
129X1/SvJ
NOD/ShiLtJ
NOD/MrkTac
PAR
Genomic Region(MHC)
Genomic Region
(DiGeorge)Genomic
Region(Ren2)
GRCm38 Alternate Loci Strains
A/JAKR/J
BALB/cCAST/Ei
129S6/SvEvTac129P2/OlaHsd129S2/SvPas129S1/SvImJ
129X1/SvJ129S7/SvEvBrd-Hprt-b-m2
NOD/MrkTacNOD/ShiLtJ
RIII
Assembly Model
Assembly Updates
Assembly (e.g. GRCm38.p5)
Primary Assembly
Unit(C57BL/6J)
Non-nuclear assembly unit
(e.g. MT)
129S6/SvEvTac
129S1/SvImJ
129X1/SvJ
NOD/ShiLtJ
NOD/MrkTac
PAR
Genomic Region(MHC)
Genomic Region
(DiGeorge)Genomic
Region(Ren2)
Patches
Genomic Region(Sftpb)
Genomic Region
(Nlrp4g)Genomic
Region(Meg3)
Patches
FIX NOVEL
SCAFFOLD STATUS AT NEXTMAJOR ASSEMBLY RELEASE
ALT LOCI
--(integrated)
Assembly Updates: Mousehttp://geval.sanger.ac.uk/index.html
http://www.ncbi.nlm.nih.gov/tools/gbench/
GRCm38.p5 Fix Patches(GCA_000001635.7)
Rims1Traf5
Ptpmt1Spata5I1
Auts2Jakmip3
Muc2Rab3aIfi30
Nadk2Ide
Assembly Updates: Mouse
GRCm39?
https://genomereference.org
INSDC Submitted Assemblies
Mouse strains poster:M5101B Will Chow
Assembly Updates: Zebrafish
GRCz11: Planned for the end of 2016
• Finish remaining clones & integrate into assembly
• Find “missing genes”• Resolve path issues• Integrate WGS into
assembly gaps• Create alternate loci for
haplotypic duplications & indels affecting gene models
• Poster: Z6085A (K. Howe)
Assembly Updates: Zebrafish
GRCz11: Planned for the end of 2016
• WTSI -> ZFIN transition• Curation: Active ->
Passive• Patch releases• Annotation: Manual ->
Automated• Ensembl• Refseq
Outline GRC Introduction Assembly updates Assembly resources
https://genomereference.org
Outline
Assembly Resources
https://genomereference.org
http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/issues/?id=MG-117
https://www.ncbi.nlm.nih.gov/Assembly name, assembly accession, organism name
(latest RefSeq)
http://www.ncbi.nlm.nih.gov/genome/tools/remap
Acknowledgements
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• Tina Graves-Lindsay• Kerstin Howe• Richard Durbin• Paul Flicek• Laura Clarke• Monte Westerfield• Deanna Church• Curators!• Developers!
GRC Mouse/Zfish Collaborators• NCBI RefSeq/Gene• HAVANA annotators• Peter Lansdorp• Mark Hills• Derek Stemple• David Page• WTSI NOD Idd team
NCBI Support• Genome Browser team• Assembly DB• Gpipe annotation team• Clone DB• Remapping Service
https://genomereference.org
For more info:poster M5055A
Utilizing NCBI Databases for Model Organism Research
News: www.ncbi.nlm.nih.gov/news/Contact us: [email protected]
Time Topic Poster Number
8:00 – 8:25 The 3 W’s of Sequence Data Submission: What, Where, and WhenIlene Mizrachi —
8:25 – 8:45Reference genome assemblies: resources and updates from the GRCValerie Schneider
M5055/A
8:45 – 9:10How to annotate for 300 species: the awesome power of NCBI’s eukaryotic genome annotation pipelineTerence Murphy
D1524/B
9:10 – 9:35 An introduction to NCBI’s RefSeq and Gene resourcesTripti Gupta
M5104/B
9:35 – 9:55 Optimizing use of NCBI databases to analyze your favorite geneNuala O’Leary
Z6088/A
