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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.


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.


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.


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.


Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly divergent genome.

Wang Y, Yu Y, Pan B, Hao P, Li Y, Shao Z, Xu X, Li X.

BMC Syst Biol. 2012;6 Suppl 3:S21. doi: 10.1186/1752-0509-6-S3-S21. Epub 2012 Dec 17.


Ragout-a reference-assisted assembly tool for bacterial genomes.

Kolmogorov M, Raney B, Paten B, Pham S.

Bioinformatics. 2014 Jun 15;30(12):i302-9. doi: 10.1093/bioinformatics/btu280.


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.


Comparing de novo assemblers for 454 transcriptome data.

Kumar S, Blaxter ML.

BMC Genomics. 2010 Oct 16;11:571. doi: 10.1186/1471-2164-11-571.


CISA: contig integrator for sequence assembly of bacterial genomes.

Lin SH, Liao YC.

PLoS One. 2013;8(3):e60843. doi: 10.1371/journal.pone.0060843. Epub 2013 Mar 28.


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.


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.


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.


InteMAP: Integrated metagenomic assembly pipeline for NGS short reads.

Lai B, Wang F, Wang X, Duan L, Zhu H.

BMC Bioinformatics. 2015 Aug 7;16:244. doi: 10.1186/s12859-015-0686-x.


Graph accordance of next-generation sequence assemblies.

Yao G, Ye L, Gao H, Minx P, Warren WC, Weinstock GM.

Bioinformatics. 2012 Jan 1;28(1):13-6. doi: 10.1093/bioinformatics/btr588. Epub 2011 Oct 23.


BASE: a practical de novo assembler for large genomes using long NGS reads.

Liu B, Liu CM, Li D, Li Y, Ting HF, Yiu SM, Luo R, Lam TW.

BMC Genomics. 2016 Aug 31;17 Suppl 5:499. doi: 10.1186/s12864-016-2829-5.


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.


The complex task of choosing a de novo assembly: lessons from fungal genomes.

Gallo JE, Muñoz JF, Misas E, McEwen JG, Clay OK.

Comput Biol Chem. 2014 Dec;53 Pt A:97-107. doi: 10.1016/j.compbiolchem.2014.08.014. Epub 2014 Aug 29.


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.


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.


LOCAS--a low coverage assembly tool for resequencing projects.

Klein JD, Ossowski S, Schneeberger K, Weigel D, Huson DH.

PLoS One. 2011;6(8):e23455. doi: 10.1371/journal.pone.0023455. Epub 2011 Aug 15.

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