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Capturing native long-range contiguity by in situ library construction and optical sequencing.

Schwartz JJ, Lee C, Hiatt JB, Adey A, Shendure J.

Proc Natl Acad Sci U S A. 2012 Nov 13;109(46):18749-54. doi: 10.1073/pnas.1202680109.


Paired-end sequencing of Fosmid libraries by Illumina.

Williams LJ, Tabbaa DG, Li N, Berlin AM, Shea TP, Maccallum I, Lawrence MS, Drier Y, Getz G, Young SK, Jaffe DB, Nusbaum C, Gnirke A.

Genome Res. 2012 Nov;22(11):2241-9. doi: 10.1101/gr.138925.112.


Is the whole greater than the sum of its parts? De novo assembly strategies for bacterial genomes based on paired-end sequencing.

Chen TW, Gan RC, Chang YF, Liao WC, Wu TH, Lee CC, Huang PJ, Lee CY, Chen YY, Chiu CH, Tang P.

BMC Genomics. 2015 Aug 28;16:648. doi: 10.1186/s12864-015-1859-8.


Local de novo assembly of RAD paired-end contigs using short sequencing reads.

Etter PD, Preston JL, Bassham S, Cresko WA, Johnson EA.

PLoS One. 2011 Apr 13;6(4):e18561. doi: 10.1371/journal.pone.0018561.


The Illumina-solexa sequencing protocol for bacterial genomes.

Hu Z, Cheng L, Wang H.

Methods Mol Biol. 2015;1231:91-7. doi: 10.1007/978-1-4939-1720-4_6.


Paired-end sequencing of long-range DNA fragments for de novo assembly of large, complex Mammalian genomes by direct intra-molecule ligation.

Asan, Geng C, Chen Y, Wu K, Cai Q, Wang Y, Lang Y, Cao H, Yang H, Wang J, Zhang X.

PLoS One. 2012;7(9):e46211. doi: 10.1371/journal.pone.0046211.


BAC sequencing using pooled methods.

Saski CA, Feltus FA, Parida L, Haiminen N.

Methods Mol Biol. 2015;1227:55-67. doi: 10.1007/978-1-4939-1652-8_3.


Comparison of sequence reads obtained from three next-generation sequencing platforms.

Suzuki S, Ono N, Furusawa C, Ying BW, Yomo T.

PLoS One. 2011;6(5):e19534. doi: 10.1371/journal.pone.0019534.


Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.

Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J.

Nat Methods. 2013 Jun;10(6):563-9. doi: 10.1038/nmeth.2474.


Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination.

Van Nieuwerburgh F, Thompson RC, Ledesma J, Deforce D, Gaasterland T, Ordoukhanian P, Head SR.

Nucleic Acids Res. 2012 Feb;40(3):e24. doi: 10.1093/nar/gkr1000.


Accurate multiplex polony sequencing of an evolved bacterial genome.

Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, Rosenbaum AM, Wang MD, Zhang K, Mitra RD, Church GM.

Science. 2005 Sep 9;309(5741):1728-32.


A new strategy for genome assembly using short sequence reads and reduced representation libraries.

Young AL, Abaan HO, Zerbino D, Mullikin JC, Birney E, Margulies EH.

Genome Res. 2010 Feb;20(2):249-56. doi: 10.1101/gr.097956.109.


De novo bacterial genome sequencing: millions of very short reads assembled on a desktop computer.

Hernandez D, François P, Farinelli L, Osterås M, Schrenzel J.

Genome Res. 2008 May;18(5):802-9. doi: 10.1101/gr.072033.107.


Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing.

Stapleton JA, Kim J, Hamilton JP, Wu M, Irber LC, Maddamsetti R, Briney B, Newton L, Burton DR, Brown CT, Chan C, Buell CR, Whitehead TA.

PLoS One. 2016 Jan 20;11(1):e0147229. doi: 10.1371/journal.pone.0147229.


Construction of bacterial artificial chromosome libraries from the parasitic nematode Brugia malayi and physical mapping of the genome of its Wolbachia endosymbiont.

Foster JM, Kumar S, Ganatra MB, Kamal IH, Ware J, Ingram J, Pope-Chappell J, Guiliano D, Whitton C, Daub J, Blaxter ML, Slatko BE.

Int J Parasitol. 2004 May;34(6):733-46.


Improving the efficiency of genomic loci capture using oligonucleotide arrays for high throughput resequencing.

Lee H, O'Connor BD, Merriman B, Funari VA, Homer N, Chen Z, Cohn DH, Nelson SF.

BMC Genomics. 2009 Dec 31;10:646. doi: 10.1186/1471-2164-10-646.


Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing.

Amini S, Pushkarev D, Christiansen L, Kostem E, Royce T, Turk C, Pignatelli N, Adey A, Kitzman JO, Vijayan K, Ronaghi M, Shendure J, Gunderson KL, Steemers FJ.

Nat Genet. 2014 Dec;46(12):1343-9. doi: 10.1038/ng.3119.


GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.

Gritsenko AA, Nijkamp JF, Reinders MJ, de Ridder D.

Bioinformatics. 2012 Jun 1;28(11):1429-37. doi: 10.1093/bioinformatics/bts175.


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