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Items: 1 to 20 of 131

1.

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline.

Treangen TJ, Koren S, Sommer DD, Liu B, Astrovskaya I, Ondov B, Darling AE, Phillippy AM, Pop M.

Genome Biol. 2013 Jan 15;14(1):R2. doi: 10.1186/gb-2013-14-1-r2.

2.

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.

3.

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
4.
5.

DIME: a novel framework for de novo metagenomic sequence assembly.

Guo X, Yu N, Ding X, Wang J, Pan Y.

J Comput Biol. 2015 Feb;22(2):159-77. doi: 10.1089/cmb.2014.0251.

6.

Sequence assembly using next generation sequencing data--challenges and solutions.

Chin FY, Leung HC, Yiu SM.

Sci China Life Sci. 2014 Nov;57(11):1140-8. doi: 10.1007/s11427-014-4752-9. Epub 2014 Oct 17. Review.

PMID:
25326069
7.

MetaCAA: A clustering-aided methodology for efficient assembly of metagenomic datasets.

Reddy RM, Mohammed MH, Mande SS.

Genomics. 2014 Feb-Mar;103(2-3):161-8. doi: 10.1016/j.ygeno.2014.02.007. Epub 2014 Mar 5.

8.

Pseudoalignment for metagenomic read assignment.

Schaeffer L, Pimentel H, Bray N, Melsted P, Pachter L.

Bioinformatics. 2017 Jul 15;33(14):2082-2088. doi: 10.1093/bioinformatics/btx106.

PMID:
28334086
9.

Binning metagenomic contigs by coverage and composition.

Alneberg J, Bjarnason BS, de Bruijn I, Schirmer M, Quick J, Ijaz UZ, Lahti L, Loman NJ, Andersson AF, Quince C.

Nat Methods. 2014 Nov;11(11):1144-6. doi: 10.1038/nmeth.3103. Epub 2014 Sep 14.

PMID:
25218180
10.

metaSPAdes: a new versatile metagenomic assembler.

Nurk S, Meleshko D, Korobeynikov A, Pevzner PA.

Genome Res. 2017 May;27(5):824-834. doi: 10.1101/gr.213959.116. Epub 2017 Mar 15.

11.

De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline.

Lin YY, Hsieh CH, Chen JH, Lu X, Kao JH, Chen PJ, Chen DS, Wang HY.

BMC Bioinformatics. 2017 Apr 26;18(1):223. doi: 10.1186/s12859-017-1630-z.

12.

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.

13.

RIEMS: a software pipeline for sensitive and comprehensive taxonomic classification of reads from metagenomics datasets.

Scheuch M, Höper D, Beer M.

BMC Bioinformatics. 2015 Mar 3;16:69. doi: 10.1186/s12859-015-0503-6.

14.

Large-scale 16S gene assembly using metagenomics shotgun sequences.

Zeng F, Wang Z, Wang Y, Zhou J, Chen T.

Bioinformatics. 2017 May 15;33(10):1447-1456. doi: 10.1093/bioinformatics/btx018.

PMID:
28158392
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.

16.

An ORFome assembly approach to metagenomics sequences analysis.

Ye Y, Tang H.

Comput Syst Bioinformatics Conf. 2008;7:3-13.

17.

EzMap: a simple pipeline for reproducible analysis of the human virome.

Czeczko P, Greenway SC, de Koning APJ.

Bioinformatics. 2017 Aug 15;33(16):2573-2574. doi: 10.1093/bioinformatics/btx202.

PMID:
28383679
18.

Assessment of metagenomic assembly using simulated next generation sequencing data.

Mende DR, Waller AS, Sunagawa S, Järvelin AI, Chan MM, Arumugam M, Raes J, Bork P.

PLoS One. 2012;7(2):e31386. doi: 10.1371/journal.pone.0031386. Epub 2012 Feb 23. Erratum in: PLoS One. 2014;9(11):e114063.

19.

LSG: An External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly.

Bonizzoni P, Vedova GD, Pirola Y, Previtali M, Rizzi R.

J Comput Biol. 2016 Mar;23(3):137-49. doi: 10.1089/cmb.2015.0172.

PMID:
26953874
20.

Reconstructing mitochondrial genomes directly from genomic next-generation sequencing reads--a baiting and iterative mapping approach.

Hahn C, Bachmann L, Chevreux B.

Nucleic Acids Res. 2013 Jul;41(13):e129. doi: 10.1093/nar/gkt371. Epub 2013 May 9.

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