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Items: 1 to 20 of 391

1.

Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer.

Peterlongo P, Chikhi R.

BMC Bioinformatics. 2012 Mar 23;13:48. doi: 10.1186/1471-2105-13-48.

2.

De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads.

Hernandez D, Tewhey R, Veyrieras JB, Farinelli L, Østerås M, François P, Schrenzel J.

Bioinformatics. 2014 Jan 1;30(1):40-9. doi: 10.1093/bioinformatics/btt590. Epub 2013 Oct 15.

PMID:
24130309
3.

Querying large read collections in main memory: a versatile data structure.

Philippe N, Salson M, Lecroq T, Léonard M, Commes T, Rivals E.

BMC Bioinformatics. 2011 Jun 17;12:242. doi: 10.1186/1471-2105-12-242.

4.

Ψ-RA: a parallel sparse index for genomic read alignment.

Oğuzhan Külekci M, Hon WK, Shah R, Scott Vitter J, Xu B.

BMC Genomics. 2011;12 Suppl 2:S7. doi: 10.1186/1471-2164-12-S2-S7. Epub 2011 Jul 27.

5.

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
6.

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. Erratum in: PLoS One. 2015;10(3):e0118741.

7.

Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools.

Kisand V, Lettieri T.

BMC Genomics. 2013 Apr 1;14:211. doi: 10.1186/1471-2164-14-211.

8.

GAM-NGS: genomic assemblies merger for next generation sequencing.

Vicedomini R, Vezzi F, Scalabrin S, Arvestad L, Policriti A.

BMC Bioinformatics. 2013;14 Suppl 7:S6. doi: 10.1186/1471-2105-14-S7-S6. Epub 2013 Apr 22.

9.

Readjoiner: a fast and memory efficient string graph-based sequence assembler.

Gonnella G, Kurtz S.

BMC Bioinformatics. 2012 May 6;13:82. doi: 10.1186/1471-2105-13-82.

10.

NeatFreq: reference-free data reduction and coverage normalization for De Novo sequence assembly.

McCorrison JM, Venepally P, Singh I, Fouts DE, Lasken RS, Methé BA.

BMC Bioinformatics. 2014 Nov 19;15:357. doi: 10.1186/s12859-014-0357-3.

11.

QC-Chain: fast and holistic quality control method for next-generation sequencing data.

Zhou Q, Su X, Wang A, Xu J, Ning K.

PLoS One. 2013;8(4):e60234. doi: 10.1371/journal.pone.0060234. Epub 2013 Apr 2.

12.

A biologist's guide to de novo genome assembly using next-generation sequence data: A test with fungal genomes.

Haridas S, Breuill C, Bohlmann J, Hsiang T.

J Microbiol Methods. 2011 Sep;86(3):368-75. doi: 10.1016/j.mimet.2011.06.019. Epub 2011 Jul 3.

PMID:
21749903
13.

Repeat-aware modeling and correction of short read errors.

Yang X, Aluru S, Dorman KS.

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S52. doi: 10.1186/1471-2105-12-S1-S52.

14.

Compareads: comparing huge metagenomic experiments.

Maillet N, Lemaitre C, Chikhi R, Lavenier D, Peterlongo P.

BMC Bioinformatics. 2012;13 Suppl 19:S10. doi: 10.1186/1471-2105-13-S19-S10. Epub 2012 Dec 19.

15.

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads.

Xie Y, Wu G, Tang J, Luo R, Patterson J, Liu S, Huang W, He G, Gu S, Li S, Zhou X, Lam TW, Li Y, Xu X, Wong GK, Wang J.

Bioinformatics. 2014 Jun 15;30(12):1660-6. doi: 10.1093/bioinformatics/btu077. Epub 2014 Feb 13.

PMID:
24532719
16.

GapFiller: a de novo assembly approach to fill the gap within paired reads.

Nadalin F, Vezzi F, Policriti A.

BMC Bioinformatics. 2012;13 Suppl 14:S8. doi: 10.1186/1471-2105-13-S14-S8. Epub 2012 Sep 7.

17.

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
18.

Scaffolding pre-assembled contigs using SSPACE.

Boetzer M, Henkel CV, Jansen HJ, Butler D, Pirovano W.

Bioinformatics. 2011 Feb 15;27(4):578-9. doi: 10.1093/bioinformatics/btq683. Epub 2010 Dec 12.

PMID:
21149342
19.

AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references.

Bao E, Jiang T, Girke T.

Bioinformatics. 2014 Jun 15;30(12):i319-i328. doi: 10.1093/bioinformatics/btu291.

20.

BLESS: bloom filter-based error correction solution for high-throughput sequencing reads.

Heo Y, Wu XL, Chen D, Ma J, Hwu WM.

Bioinformatics. 2014 May 15;30(10):1354-62. doi: 10.1093/bioinformatics/btu030. Epub 2014 Jan 21.

PMID:
24451628

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