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Results: 1 to 20 of 93

1.

Ray Meta: scalable de novo metagenome assembly and profiling.

Boisvert S, Raymond F, Godzaridis E, Laviolette F, Corbeil J.

Genome Biol. 2012 Dec 22;13(12):R122. doi: 10.1186/gb-2012-13-12-r122.

PMID:
23259615
[PubMed - in process]
Free PMC Article
2.

Software for pre-processing Illumina next-generation sequencing short read sequences.

Chen C, Khaleel SS, Huang H, Wu CH.

Source Code Biol Med. 2014 May 3;9:8. doi: 10.1186/1751-0473-9-8. eCollection 2014.

PMID:
24955109
[PubMed]
Free PMC Article
3.

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.

PMID:
21989307
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies.

Boisvert S, Laviolette F, Corbeil J.

J Comput Biol. 2010 Nov;17(11):1519-33. doi: 10.1089/cmb.2009.0238. Epub 2010 Oct 20.

PMID:
20958248
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

An extended genovo metagenomic assembler by incorporating paired-end information.

Afiahayati, Sato K, Sakakibara Y.

PeerJ. 2013 Oct 31;1:e196. doi: 10.7717/peerj.196. eCollection 2013.

PMID:
24281688
[PubMed]
Free PMC Article
6.

Parallelized short read assembly of large genomes using de Bruijn graphs.

Liu Y, Schmidt B, Maskell DL.

BMC Bioinformatics. 2011 Aug 25;12:354. doi: 10.1186/1471-2105-12-354.

PMID:
21867511
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

PRICE: software for the targeted assembly of components of (Meta) genomic sequence data.

Ruby JG, Bellare P, Derisi JL.

G3 (Bethesda). 2013 May 20;3(5):865-80. doi: 10.1534/g3.113.005967.

PMID:
23550143
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Meta-IDBA: a de Novo assembler for metagenomic data.

Peng Y, Leung HC, Yiu SM, Chin FY.

Bioinformatics. 2011 Jul 1;27(13):i94-101. doi: 10.1093/bioinformatics/btr216.

PMID:
21685107
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data.

Zhang Y, Sun Y, Cole JR.

PLoS Comput Biol. 2014 Aug 14;10(8):e1003737. doi: 10.1371/journal.pcbi.1003737. eCollection 2014 Aug.

PMID:
25122209
[PubMed - in process]
Free PMC Article
10.

Omega: an Overlap-graph de novo Assembler for Metagenomics.

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

Bioinformatics. 2014 Jun 19. pii: btu395. [Epub ahead of print]

PMID:
24947750
[PubMed - as supplied by publisher]
11.

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.

Peng Y, Leung HC, Yiu SM, Chin FY.

Bioinformatics. 2012 Jun 1;28(11):1420-8. doi: 10.1093/bioinformatics/bts174. Epub 2012 Apr 11.

PMID:
22495754
[PubMed - indexed for MEDLINE]
Free Article
12.

Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms.

Haznedaroglu BZ, Reeves D, Rismani-Yazdi H, Peccia J.

BMC Bioinformatics. 2012 Jul 18;13:170. doi: 10.1186/1471-2105-13-170.

PMID:
22808927
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Parallel-META: efficient metagenomic data analysis based on high-performance computation.

Su X, Xu J, Ning K.

BMC Syst Biol. 2012 Jul 16;6 Suppl 1:S16. doi: 10.1186/1752-0509-6-S1-S16. Epub 2012 Jul 16.

PMID:
23046922
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
22821567
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Genovo: de novo assembly for metagenomes.

Laserson J, Jojic V, Koller D.

J Comput Biol. 2011 Mar;18(3):429-43. doi: 10.1089/cmb.2010.0244.

PMID:
21385045
[PubMed - indexed for MEDLINE]
16.

Gossamer--a resource-efficient de novo assembler.

Conway T, Wazny J, Bromage A, Zobel J, Beresford-Smith B.

Bioinformatics. 2012 Jul 15;28(14):1937-8. doi: 10.1093/bioinformatics/bts297. Epub 2012 May 18.

PMID:
22611131
[PubMed - indexed for MEDLINE]
Free Article
17.

ABySS: a parallel assembler for short read sequence data.

Simpson JT, Wong K, Jackman SD, Schein JE, Jones SJ, Birol I.

Genome Res. 2009 Jun;19(6):1117-23. doi: 10.1101/gr.089532.108. Epub 2009 Feb 27.

PMID:
19251739
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Assembler for de novo assembly of large genomes.

Chu TC, Lu CH, Liu T, Lee GC, Li WH, Shih AC.

Proc Natl Acad Sci U S A. 2013 Sep 3;110(36):E3417-24. doi: 10.1073/pnas.1314090110. Epub 2013 Aug 21.

PMID:
23966565
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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.

PMID:
22847406
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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.

PMID:
23593174
[PubMed - indexed for MEDLINE]
Free PMC Article

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