Haplotype-resolved genome sequencing of a Gujarati Indian individual

Levy, S. et al. The diploid genome sequence of an individual human. PLoS Biol. 5, e254 (2007).

International HapMap Consortium. Integrating common and rare genetic variation in diverse human populations. Nature 467, 52–58 (2010).

Green, R.E. et al. A draft sequence of the Neandertal genome. Science 328, 710–722 (2010).

Anonymous. Human genome: Genomes by the thousand. Nature 467, 1026–1027 (2010).

Shendure, J. & Ji, H. Next-generation DNA sequencing. Nat. Biotechnol. 26, 1135–1145 (2008).

Kidd, J.M. et al. Mapping and sequencing of structural variation from eight human genomes. Nature 453, 56–64 (2008).

Li, R. et al. Building the sequence map of the human pan-genome. Nat. Biotechnol. 28, 57–63 (2010).

Kidd, J.M. et al. Characterization of missing human genome sequences and copy-number polymorphic insertions. Nat. Methods 7, 365–371 (2010).

International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001).

McKernan, K.J. et al. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res. 19, 1527–1541 (2009).

Schatz, M.C., Delcher, A.L. & Salzberg, S.L. Assembly of large genomes using second-generation sequencing. Genome Res. 20, 1165–1173 (2010).

Wang, J. et al. The diploid genome sequence of an Asian individual. Nature 456, 60–65 (2008).

Roach, J.C. et al. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328, 636–639 (2010).

1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467, 1061–1073 (2010).

Reich, D., Thangaraj, K., Patterson, N., Price, A.L. & Singh, L. Reconstructing Indian population history. Nature 461, 489–494 (2009).

Adey, A. et al. Rapid, low-input, low-bias construction of shotgun fragment libraries by high density in vitro transposition. Genome Biol. 11, R119 (2010).

Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).

Bansal, V. & Bafna, V. HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. Bioinformatics 24, i153–i159 (2008).

Kim, J.H., Waterman, M.S. & Li, L.M. Diploid genome reconstruction of Ciona intestinalis and comparative analysis with Ciona savignyi. Genome Res. 17, 1101–1110 (2007).

Bansal, V., Halpern, A.L., Axelrod, N. & Bafna, V. An MCMC algorithm for haplotype assembly from whole-genome sequence data. Genome Res. 18, 1336–1346 (2008).

Alkan, C. et al. Personalized copy number and segmental duplication maps using next-generation sequencing. Nat. Genet. 41, 1061–1067 (2009).

Hormozdiari, F. et al. Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics 26, i350–i357 (2010).

Zody, M.C. et al. Evolutionary toggling of the MAPT 17q21.31 inversion region. Nat. Genet. 40, 1076–1083 (2008).

Ng, S.B. et al. Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461, 272–276 (2009).

Ng, S.B. et al. Exome sequencing identifies the cause of a mendelian disorder. Nat. Genet. 42, 30–35 (2010).

Drysdale, C.M. et al. Complex promoter and coding region beta 2-adrenergic receptor haplotypes alter receptor expression and predict in vivo responsiveness. Proc. Natl. Acad. Sci. USA 97, 10483–10488 (2000).

Korbel, J.O. et al. Paired-end mapping reveals extensive structural variation in the human genome. Science 318, 420–426 (2007).

Ma, L. et al. Direct determination of molecular haplotypes by chromosome microdissection. Nat. Methods 7, 299–301 (2010).

Tycko, B. Allele-specific DNA methylation: beyond imprinting. Hum. Mol. Genet. 19, R210–R220 (2010).

Raymond, C.K. et al. Targeted, haplotype-resolved resequencing of long segments of the human genome. Genomics 86, 759–766 (2005).

Sudmant, P.H. et al. Diversity of human copy number variation and multicopy genes. Science 330, 641–646 (2010).

Zerbino, D.R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821–829 (2008).