We constructed a hybrid de novo assembly combining 5.4 Gbp of capillary read pairs with the contigs from an initial short read assembly of 166.8 Gbp of Illumina paired reads. Improvements in long-range structure were then guided by human homology, placing contigs into scaffolds wherever read pairs confirmed collinearity between gorilla and human. Base-pair contiguity was improved by local reassembly within each scaffold, merging or extending contigs using Illumina read pairs. Finally we used additional Kamilah BAC and fosmid end pair capillary sequences to provide longer range scaffolding. Base errors were corrected by mapping all Illumina reads back to the assembly and rectifying apparent homozygous variants, while recording the location of heterozygous sites. Further details and other methods are described in Supplementary Information.
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Scally A., Dutheil J.Y., Hillier L.W., Jordan G.E., Goodhead I., Herrero J., Hobolth A., Lappalainen T., Mailund T., Marques-Bonet T., McCarthy S., Montgomery S.H., Schwalie P.C., Tang Y.A., Ward M.C., Xue Y., Yngvadottir B., Alkan C., Andersen L.N., Ayub Q., Ball E.V., Beal K., Bradley B.J., Chen Y., Clee C.M., Fitzgerald S., Graves T.A., Gu Y., Heath P., Heger A., Karakoc E., Kolb-Kokocinski A., Laird G.K., Lunter G., Meader S., Mort M., Mullikin J.C., Munch K., O’Connor T.D., Phillips A.D., Prado-Martinez J., Rogers A.S., Sajjadian S., Schmidt D., Shaw K., Simpson J.T., Stenson P.D., Turner D.J., Vigilant L., Vilella A.J., Whitener W., Zhu B., Cooper D.N., de Jong P., Dermitzakis E.T., Eichler E.E., Flicek P., Goldman N., Mundy N.I., Ning Z., Odom D.T., Ponting C.P., Quail M.A., Ryder O.A., Searle S.M., Warren W.C., Wilson R.K., Schierup M.H., Rogers J., Tyler-Smith C, & Durbin R. (2012). Insights into hominid evolution from the gorilla genome sequence. Nature, 483(7388), 169-175.
Publication 2012
Base pair Capillary Gorilla Heterozygous Homozygous Human Hybrid
Corresponding Organization :
Other organizations :
Wellcome Sanger Institute, Aarhus University, University of Washington, European Bioinformatics Institute, Wellcome Trust, University of Geneva, University of Cambridge, Hutchison/MRC Research Centre, Cardiff University, Washington University in St. Louis, University of Oxford, Genomics (United Kingdom), Wellcome Centre for Human Genetics, National Human Genome Research Institute, National Institutes of Health, Institut de Biologia Evolutiva, Max Planck Institute for Evolutionary Anthropology, Howard Hughes Medical Institute, Cancer Research UK, San Diego Zoo Institute for Conservation Research
Kamilah BAC and fosmid end pair capillary sequences
dependent variables
Contigs from an initial short read assembly
Scaffolds with improved long-range structure
Base-pair contiguity improved by local reassembly within each scaffold
Base errors corrected by mapping all Illumina reads back to the assembly and rectifying apparent homozygous variants
control variables
Human homology used to guide placement of contigs into scaffolds
Read pairs used to confirm collinearity between gorilla and human
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