High-resolution comparative analysis of great ape genomes
Data, tables, and code
Zev N. Kronenberg, Ian T. Fiddes, David Gordon, Shwetha Murali, Stuart Cantsilieris,
Olivia S. Meyerson, Jason G. Underwood, Bradley J. Nelson, Mark J.P. Chaisson, Max L. Dougherty,
Katherine M. Munson, Alex R. Hastie, Mark Diekhans, Fereydoun Hormozdiari, Nicola Lorusso,
Kendra Hoekzema, Ruolan Qiu, Karen Clark, Archana Raja, AnneMarie E. Welch, Melanie Sorensen,
Carl Baker, Robert S. Fulton, Joel Armstrong, Tina A. Graves-Lindsay, Ahmet M. Denli,
Emma R. Hoppe, PingHsun Hsieh, Christopher M. Hill, Andy Wing Chun Pang, Joyce Lee,
Ernest T. Lam, Susan K. Dutcher, Fred H. Gage, Wesley C. Warren, Jay Shendure, David Haussler,
Valerie A. Schneider, Han Cao, Mario Ventura, Richard K. Wilson, Benedict Paten, Alex Pollen,
and Evan E. Eichler
Data
- orangutan assembled chromosomes Susie_PABv2
- chimpanzee assembled chromosomes Clint_PTRv2
- orangutan indel-corrected contigs (v2)
- chimpanzee indel-corrected contigs (v2)
- BLASR alignments
- CCDS Multiple Sequence Alignments
- Random Multiple Sequence Alignments
- Genome-Wide Multiple Sequence Alignments
- Unannotated VCF of structural variants
(Tabix index)
- VEP-annotated VCF of structural variants
(Tabix index)
- Orangutan clones for FISH ordering
- Chimpanzee clones for FISH ordering
- Human clones for FISH ordering
- Full-length non-chimeric reads (Human, Chimp, Gorilla, Orang)
- ICE collapsed isoforms (Human, Chimp, Gorilla, Orang)
- CAT annotated gene models (gtf|gff3) (Chimp, Gorilla, Orang)(Chimp, Gorilla, Orang)
- Repeat masker (Chimp,Orang)
- Tandem repeat finder (Chimp,Orang)
- Liftover chain for raw contigs to cut,indel-corrected 'final' NCBI contigs
- Trees, code, and summary file for ILS analysis
Tables
Code and supplementary analysis
For more information or help with any of these resources, please contact: smurali [ a t ] uw.edu