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The anatomy of successful computational biology software.
Altschul S, Demchak B, Durbin R, Gentleman R, Krzywinski M, Li H, Nekrutenko A, Robinson J, Rasband W, Taylor J, Trapnell C. Altschul S, et al. Among authors: li h. Nat Biotechnol. 2013 Oct;31(10):894-7. doi: 10.1038/nbt.2721. Nat Biotechnol. 2013. PMID: 24104757 Free PMC article. No abstract available.
The Sequence Alignment/Map format and SAMtools.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. Li H, et al. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. Bioinformatics. 2009. PMID: 19505943 Free PMC article.
A map of human genome variation from population-scale sequencing.
1000 Genomes Project Consortium; Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA, Hurles ME, McVean GA. 1000 Genomes Project Consortium, et al. Nature. 2010 Oct 28;467(7319):1061-73. doi: 10.1038/nature09534. Nature. 2010. PMID: 20981092 Free PMC article.
The 1000 Genomes Project: data management and community access.
Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, Vaughan B, Preuss D, Leinonen R, Shumway M, Sherry S, Flicek P; 1000 Genomes Project Consortium. Clarke L, et al. Nat Methods. 2012 Apr 27;9(5):459-62. doi: 10.1038/nmeth.1974. Nat Methods. 2012. PMID: 22543379 Free PMC article.
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.
Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, Fulton RS, Kremitzki M, Magrini V, Markovic C, McGrath S, Steinberg KM, Auger K, Chow W, Collins J, Harden G, Hubbard T, Pelan S, Simpson JT, Threadgold G, Torrance J, Wood JM, Clarke L, Koren S, Boitano M, Peluso P, Li H, Chin CS, Phillippy AM, Durbin R, Wilson RK, Flicek P, Eichler EE, Church DM. Schneider VA, et al. Among authors: li h. Genome Res. 2017 May;27(5):849-864. doi: 10.1101/gr.213611.116. Epub 2017 Apr 10. Genome Res. 2017. PMID: 28396521 Free PMC article.
htsget: a protocol for securely streaming genomic data.
Kelleher J, Lin M, Albach CH, Birney E, Davies R, Gourtovaia M, Glazer D, Gonzalez CY, Jackson DK, Kemp A, Marshall J, Nowak A, Senf A, Tovar-Corona JM, Vikhorev A, Keane TM; GA4GH Streaming Task Team. Kelleher J, et al. Bioinformatics. 2019 Jan 1;35(1):119-121. doi: 10.1093/bioinformatics/bty492. Bioinformatics. 2019. PMID: 29931085 Free PMC article.
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