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Spaced Seed Data Structures for De Novo Assembly.

Birol I, Chu J, Mohamadi H, Jackman SD, Raghavan K, Vandervalk BP, Raymond A, Warren RL.

Int J Genomics. 2015;2015:196591. doi: 10.1155/2015/196591. Epub 2015 Oct 11.


Playing hide and seek with repeats in local and global de novo transcriptome assembly of short RNA-seq reads.

Lima L, Sinaimeri B, Sacomoto G, Lopez-Maestre H, Marchet C, Miele V, Sagot MF, Lacroix V.

Algorithms Mol Biol. 2017 Feb 22;12:2. doi: 10.1186/s13015-017-0091-2. eCollection 2017.


SOPRA: Scaffolding algorithm for paired reads via statistical optimization.

Dayarian A, Michael TP, Sengupta AM.

BMC Bioinformatics. 2010 Jun 24;11:345. doi: 10.1186/1471-2105-11-345.


Pseudo-Sanger sequencing: massively parallel production of long and near error-free reads using NGS technology.

Ruan J, Jiang L, Chong Z, Gong Q, Li H, Li C, Tao Y, Zheng C, Zhai W, Turissini D, Cannon CH, Lu X, Wu CI.

BMC Genomics. 2013 Oct 17;14:711. doi: 10.1186/1471-2164-14-711.


Effective de novo assembly of fish genome using haploid larvae.

Iwasaki Y, Nishiki I, Nakamura Y, Yasuike M, Kai W, Nomura K, Yoshida K, Nomura Y, Fujiwara A, Kobayashi T, Ototake M.

Gene. 2016 Feb 1;576(2 Pt 1):644-9. doi: 10.1016/j.gene.2015.10.015. Epub 2015 Oct 23.


Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations.

García-López R, Vázquez-Castellanos JF, Moya A.

Front Bioeng Biotechnol. 2015 Sep 17;3:141. doi: 10.3389/fbioe.2015.00141. eCollection 2015.


FMLRC: Hybrid long read error correction using an FM-index.

Wang JR, Holt J, McMillan L, Jones CD.

BMC Bioinformatics. 2018 Feb 9;19(1):50. doi: 10.1186/s12859-018-2051-3.


MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads.

Namiki T, Hachiya T, Tanaka H, Sakakibara Y.

Nucleic Acids Res. 2012 Nov 1;40(20):e155. doi: 10.1093/nar/gks678. Epub 2012 Jul 19.


Efficient de novo assembly of large genomes using compressed data structures.

Simpson JT, Durbin R.

Genome Res. 2012 Mar;22(3):549-56. doi: 10.1101/gr.126953.111. Epub 2011 Dec 7.


Semantic Assembly and Annotation of Draft RNAseq Transcripts without a Reference Genome.

Ptitsyn A, Temanni R, Bouchard C, Anderson PA.

PLoS One. 2015 Sep 22;10(9):e0138006. doi: 10.1371/journal.pone.0138006. eCollection 2015.


HyDA-Vista: towards optimal guided selection of k-mer size for sequence assembly.

Shariat B, Movahedi NS, Chitsaz H, Boucher C.

BMC Genomics. 2014;15 Suppl 10:S9. doi: 10.1186/1471-2164-15-S10-S9. Epub 2014 Dec 12.


Identification of optimum sequencing depth especially for de novo genome assembly of small genomes using next generation sequencing data.

Desai A, Marwah VS, Yadav A, Jha V, Dhaygude K, Bangar U, Kulkarni V, Jere A.

PLoS One. 2013 Apr 12;8(4):e60204. doi: 10.1371/journal.pone.0060204. Print 2013.


Konnector v2.0: pseudo-long reads from paired-end sequencing data.

Vandervalk BP, Yang C, Xue Z, Raghavan K, Chu J, Mohamadi H, Jackman SD, Chiu R, Warren RL, Birol I.

BMC Med Genomics. 2015;8 Suppl 3:S1. doi: 10.1186/1755-8794-8-S3-S1. Epub 2015 Sep 23.


Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers.

Medvedev P, Pham S, Chaisson M, Tesler G, Pevzner P.

J Comput Biol. 2011 Nov;18(11):1625-34. doi: 10.1089/cmb.2011.0151. Epub 2011 Oct 14.


A computer simulator for assessing different challenges and strategies of de novo sequence assembly.

Knudsen B, Forsberg R, Miyamoto MM.

Genes (Basel). 2010 Sep 13;1(2):263-82. doi: 10.3390/genes1020263.


Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage.

Holley G, Wittler R, Stoye J.

Algorithms Mol Biol. 2016 Apr 14;11:3. doi: 10.1186/s13015-016-0066-8. eCollection 2016.


Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of de novo assemblers.

Amin S, Prentis PJ, Gilding EK, Pavasovic A.

BMC Res Notes. 2014 Aug 1;7:488. doi: 10.1186/1756-0500-7-488.


Efficient construction of an assembly string graph using the FM-index.

Simpson JT, Durbin R.

Bioinformatics. 2010 Jun 15;26(12):i367-73. doi: 10.1093/bioinformatics/btq217.


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.


Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs.

Kundeti VK, Rajasekaran S, Dinh H, Vaughn M, Thapar V.

BMC Bioinformatics. 2010 Nov 15;11:560. doi: 10.1186/1471-2105-11-560.

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