Format
Items per page
Sort by

Send to:

Choose Destination

Links from PubMed

Items: 1 to 20 of 136

1.

Scaling metagenome sequence assembly with probabilistic de Bruijn graphs.

Pell J, Hintze A, Canino-Koning R, Howe A, Tiedje JM, Brown CT.

Proc Natl Acad Sci U S A. 2012 Aug 14;109(33):13272-7. doi: 10.1073/pnas.1121464109. Epub 2012 Jul 30.

2.

Evaluation of short read metagenomic assembly.

Charuvaka A, Rangwala H.

BMC Genomics. 2011;12 Suppl 2:S8. doi: 10.1186/1471-2164-12-S2-S8. Epub 2011 Jul 27.

3.

Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

Zerbino DR, Birney E.

Genome Res. 2008 May;18(5):821-9. doi: 10.1101/gr.074492.107. Epub 2008 Mar 18.

4.

Compact representation of k-mer de Bruijn graphs for genome read assembly.

Rødland EA.

BMC Bioinformatics. 2013 Oct 23;14:313. doi: 10.1186/1471-2105-14-313.

5.

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.

6.

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.

7.

Exploiting sparseness in de novo genome assembly.

Ye C, Ma ZS, Cannon CH, Pop M, Yu DW.

BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S1. doi: 10.1186/1471-2105-13-S6-S1.

8.

ALLPATHS: de novo assembly of whole-genome shotgun microreads.

Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB.

Genome Res. 2008 May;18(5):810-20. doi: 10.1101/gr.7337908. Epub 2008 Mar 13.

9.

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.

10.

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.

11.

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.

12.

Succinct data structures for assembling large genomes.

Conway TC, Bromage AJ.

Bioinformatics. 2011 Feb 15;27(4):479-86. doi: 10.1093/bioinformatics/btq697. Epub 2011 Jan 17.

13.

Space-efficient and exact de Bruijn graph representation based on a Bloom filter.

Chikhi R, Rizk G.

Algorithms Mol Biol. 2013 Sep 16;8(1):22. doi: 10.1186/1748-7188-8-22.

14.

The de novo assembly of mitochondrial genomes of the extinct passenger pigeon (Ectopistes migratorius) with next generation sequencing.

Hung CM, Lin RC, Chu JH, Yeh CF, Yao CJ, Li SH.

PLoS One. 2013;8(2):e56301. doi: 10.1371/journal.pone.0056301. Epub 2013 Feb 20.

15.

Omega: an overlap-graph de novo assembler for metagenomics.

Haider B, Ahn TH, Bushnell B, Chai J, Copeland A, Pan C.

Bioinformatics. 2014 Oct;30(19):2717-22. doi: 10.1093/bioinformatics/btu395. Epub 2014 Jun 19.

16.

Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study.

Cerdeira LT, Carneiro AR, Ramos RT, de Almeida SS, D'Afonseca V, Schneider MP, Baumbach J, Tauch A, McCulloch JA, Azevedo VA, Silva A.

J Microbiol Methods. 2011 Aug;86(2):218-23. doi: 10.1016/j.mimet.2011.05.008. Epub 2011 May 18.

17.

De novo fragment assembly with short mate-paired reads: Does the read length matter?

Chaisson MJ, Brinza D, Pevzner PA.

Genome Res. 2009 Feb;19(2):336-46. doi: 10.1101/gr.079053.108. Epub 2008 Dec 3.

18.

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets.

Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo MJ, Dupont CL, Badger JH, Novotny M, Rusch DB, Fraser LJ, Gormley NA, Schulz-Trieglaff O, Smith GP, Evers DJ, Pevzner PA, Lasken RS.

Nat Biotechnol. 2011 Sep 18;29(10):915-21. doi: 10.1038/nbt.1966.

19.

Advances in computational analysis of metagenome sequences.

Davenport CF, Tümmler B.

Environ Microbiol. 2013 Jan;15(1):1-5. doi: 10.1111/j.1462-2920.2012.02843.x. Epub 2012 Aug 8.

PMID:
22882611
20.

On the representation of de Bruijn graphs.

Chikhi R, Limasset A, Jackman S, Simpson JT, Medvedev P.

J Comput Biol. 2015 May;22(5):336-52. doi: 10.1089/cmb.2014.0160. Epub 2015 Jan 28.

PMID:
25629448
Format
Items per page
Sort by

Send to:

Choose Destination

Supplemental Content

Write to the Help Desk