Display Settings:

Format
Items per page
Sort by

Send to:

Choose Destination

Results: 1 to 20 of 90

1.

CGAL: computing genome assembly likelihoods.

Rahman A, Pachter L.

Genome Biol. 2013 Jan 29;14(1):R8. doi: 10.1186/gb-2013-14-1-r8.

PMID:
23360652
[PubMed - in process]
Free PMC Article
2.

Identification of novel transcripts in annotated genomes using RNA-Seq.

Roberts A, Pimentel H, Trapnell C, Pachter L.

Bioinformatics. 2011 Sep 1;27(17):2325-9. doi: 10.1093/bioinformatics/btr355. Epub 2011 Jun 21.

PMID:
21697122
[PubMed - indexed for MEDLINE]
Free Article
3.

QUAST: quality assessment tool for genome assemblies.

Gurevich A, Saveliev V, Vyahhi N, Tesler G.

Bioinformatics. 2013 Apr 15;29(8):1072-5. doi: 10.1093/bioinformatics/btt086. Epub 2013 Feb 19.

PMID:
23422339
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Assessing De Novo transcriptome assembly metrics for consistency and utility.

O'Neil ST, Emrich SJ.

BMC Genomics. 2013 Jul 9;14:465. doi: 10.1186/1471-2164-14-465.

PMID:
23837739
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

De novo likelihood-based measures for comparing genome assemblies.

Ghodsi M, Hill CM, Astrovskaya I, Lin H, Sommer DD, Koren S, Pop M.

BMC Res Notes. 2013 Aug 22;6:334. doi: 10.1186/1756-0500-6-334.

PMID:
23965294
[PubMed - in process]
Free PMC Article
6.

Evaluating characteristics of de novo assembly software on 454 transcriptome data: a simulation approach.

Mundry M, Bornberg-Bauer E, Sammeth M, Feulner PG.

PLoS One. 2012;7(2):e31410. doi: 10.1371/journal.pone.0031410. Epub 2012 Feb 27.

PMID:
22384018
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Finishing bacterial genome assemblies with Mix.

Soueidan H, Maurier F, Groppi A, Sirand-Pugnet P, Tardy F, Citti C, Dupuy V, Nikolski M.

BMC Bioinformatics. 2013;14 Suppl 15:S16. doi: 10.1186/1471-2105-14-S15-S16. Epub 2013 Oct 15.

PMID:
24564706
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers.

Jünemann S, Prior K, Albersmeier A, Albaum S, Kalinowski J, Goesmann A, Stoye J, Harmsen D.

PLoS One. 2014 Sep 8;9(9):e107014. doi: 10.1371/journal.pone.0107014. eCollection 2014.

PMID:
25198770
[PubMed - in process]
Free PMC Article
9.

Assemblathon 1: a competitive assessment of de novo short read assembly methods.

Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B.

Genome Res. 2011 Dec;21(12):2224-41. doi: 10.1101/gr.126599.111. Epub 2011 Sep 16.

PMID:
21926179
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Assembly reconciliation.

Zimin AV, Smith DR, Sutton G, Yorke JA.

Bioinformatics. 2008 Jan 1;24(1):42-5. Epub 2007 Dec 5.

PMID:
18057021
[PubMed - indexed for MEDLINE]
Free Article
11.

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
12.

Comparing de novo genome assembly: the long and short of it.

Narzisi G, Mishra B.

PLoS One. 2011 Apr 29;6(4):e19175. doi: 10.1371/journal.pone.0019175.

PMID:
21559467
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Mauve assembly metrics.

Darling AE, Tritt A, Eisen JA, Facciotti MT.

Bioinformatics. 2011 Oct 1;27(19):2756-7. doi: 10.1093/bioinformatics/btr451. Epub 2011 Aug 2.

PMID:
21810901
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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
15.

Distilled single-cell genome sequencing and de novo assembly for sparse microbial communities.

Taghavi Z, Movahedi NS, Draghici S, Chitsaz H.

Bioinformatics. 2013 Oct 1;29(19):2395-401. doi: 10.1093/bioinformatics/btt420. Epub 2013 Aug 5.

PMID:
23918251
[PubMed - indexed for MEDLINE]
16.

Exploring genome characteristics and sequence quality without a reference.

Simpson JT.

Bioinformatics. 2014 May 1;30(9):1228-35. doi: 10.1093/bioinformatics/btu023. Epub 2014 Jan 17.

PMID:
24443382
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Arapan-S: a fast and highly accurate whole-genome assembly software for viruses and small genomes.

Sahli M, Shibuya T.

BMC Res Notes. 2012 May 16;5:243. doi: 10.1186/1756-0500-5-243.

PMID:
22591859
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

A de novo metagenomic assembly program for shotgun DNA reads.

Lai B, Ding R, Li Y, Duan L, Zhu H.

Bioinformatics. 2012 Jun 1;28(11):1455-62. doi: 10.1093/bioinformatics/bts162. Epub 2012 Apr 11.

PMID:
22495746
[PubMed - indexed for MEDLINE]
Free Article
19.

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.

PMID:
22537038
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

LTC: a novel algorithm to improve the efficiency of contig assembly for physical mapping in complex genomes.

Frenkel Z, Paux E, Mester D, Feuillet C, Korol A.

BMC Bioinformatics. 2010 Nov 30;11:584. doi: 10.1186/1471-2105-11-584.

PMID:
21118513
[PubMed - indexed for MEDLINE]
Free PMC Article

Display Settings:

Format
Items per page
Sort by

Send to:

Choose Destination

Supplemental Content

Write to the Help Desk