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Items: 1 to 20 of 193


Reducing assembly complexity of microbial genomes with single-molecule sequencing.

Koren S, Harhay GP, Smith TP, Bono JL, Harhay DM, Mcvey SD, Radune D, Bergman NH, Phillippy AM.

Genome Biol. 2013;14(9):R101.


One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly.

Koren S, Phillippy AM.

Curr Opin Microbiol. 2015 Feb;23:110-20. doi: 10.1016/j.mib.2014.11.014. Epub 2014 Dec 1. Review.


Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology.

English AC, Richards S, Han Y, Wang M, Vee V, Qu J, Qin X, Muzny DM, Reid JG, Worley KC, Gibbs RA.

PLoS One. 2012;7(11):e47768. doi: 10.1371/journal.pone.0047768. Epub 2012 Nov 21.


Evaluation and Validation of Assembling Corrected PacBio Long Reads for Microbial Genome Completion via Hybrid Approaches.

Lin HH, Liao YC.

PLoS One. 2015 Dec 7;10(12):e0144305. doi: 10.1371/journal.pone.0144305. eCollection 2015.


SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information.

Boetzer M, Pirovano W.

BMC Bioinformatics. 2014 Jun 20;15:211. doi: 10.1186/1471-2105-15-211.


A hybrid approach for the automated finishing of bacterial genomes.

Bashir A, Klammer A, Robins WP, Chin CS, Webster D, Paxinos E, Hsu D, Ashby M, Wang S, Peluso P, Sebra R, Sorenson J, Bullard J, Yen J, Valdovino M, Mollova E, Luong K, Lin S, LaMay B, Joshi A, Rowe L, Frace M, Tarr CL, Turnsek M, Davis BM, Kasarskis A, Mekalanos JJ, Waldor MK, Schadt EE.

Nat Biotechnol. 2012 Jul 1;30(7):701-707. doi: 10.1038/nbt.2288.


FGAP: an automated gap closing tool.

Piro VC, Faoro H, Weiss VA, Steffens MB, Pedrosa FO, Souza EM, Raittz RT.

BMC Res Notes. 2014 Jun 18;7:371. doi: 10.1186/1756-0500-7-371.


Subset selection of high-depth next generation sequencing reads for de novo genome assembly using MapReduce framework.

Fang CH, Chang YJ, Chung WC, Hsieh PH, Lin CY, Ho JM.

BMC Genomics. 2015;16 Suppl 12:S9. doi: 10.1186/1471-2164-16-S12-S9. Epub 2015 Dec 9.


An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome.

Ferrarini M, Moretto M, Ward JA, Šurbanovski N, Stevanović V, Giongo L, Viola R, Cavalieri D, Velasco R, Cestaro A, Sargent DJ.

BMC Genomics. 2013 Oct 1;14:670. doi: 10.1186/1471-2164-14-670.


A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs.

Swain MT, Tsai IJ, Assefa SA, Newbold C, Berriman M, Otto TD.

Nat Protoc. 2012 Jun 7;7(7):1260-84. doi: 10.1038/nprot.2012.068.


Completing bacterial genome assemblies: strategy and performance comparisons.

Liao YC, Lin SH, Lin HH.

Sci Rep. 2015 Mar 4;5:8747. doi: 10.1038/srep08747.


Efficient and accurate whole genome assembly and methylome profiling of E. coli.

Powers JG, Weigman VJ, Shu J, Pufky JM, Cox D, Hurban P.

BMC Genomics. 2013 Oct 3;14:675. doi: 10.1186/1471-2164-14-675.


Short read fragment assembly of bacterial genomes.

Chaisson MJ, Pevzner PA.

Genome Res. 2008 Feb;18(2):324-30. Epub 2007 Dec 14.


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.


The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation.

Mavromatis K, Land ML, Brettin TS, Quest DJ, Copeland A, Clum A, Goodwin L, Woyke T, Lapidus A, Klenk HP, Cottingham RW, Kyrpides NC.

PLoS One. 2012;7(12):e48837. doi: 10.1371/journal.pone.0048837. Epub 2012 Dec 12.


OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees.

Gao S, Bertrand D, Chia BK, Nagarajan N.

Genome Biol. 2016 May 11;17:102. doi: 10.1186/s13059-016-0951-y.


Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome.

Faino L, Seidl MF, Datema E, van den Berg GC, Janssen A, Wittenberg AH, Thomma BP.

MBio. 2015 Aug 18;6(4). pii: e00936-15. doi: 10.1128/mBio.00936-15.


Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies.

Wetzel J, Kingsford C, Pop M.

BMC Bioinformatics. 2011 Apr 13;12:95. doi: 10.1186/1471-2105-12-95.


Genome assembly using Nanopore-guided long and error-free DNA reads.

Madoui MA, Engelen S, Cruaud C, Belser C, Bertrand L, Alberti A, Lemainque A, Wincker P, Aury JM.

BMC Genomics. 2015 Apr 20;16:327. doi: 10.1186/s12864-015-1519-z.


Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps.

Tsai IJ, Otto TD, Berriman M.

Genome Biol. 2010;11(4):R41. doi: 10.1186/gb-2010-11-4-r41. Epub 2010 Apr 13.

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