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Items: 1 to 20 of 184

1.

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.

2.

drVM: a new tool for efficient genome assembly of known eukaryotic viruses from metagenomes.

Lin HH, Liao YC.

Gigascience. 2017 Feb 1;6(2):1-10. doi: 10.1093/gigascience/gix003.

3.

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.

4.

Estimating DNA coverage and abundance in metagenomes using a gamma approximation.

Hooper SD, Dalevi D, Pati A, Mavromatis K, Ivanova NN, Kyrpides NC.

Bioinformatics. 2010 Feb 1;26(3):295-301. doi: 10.1093/bioinformatics/btp687. Epub 2009 Dec 14.

5.

Grid-Assembly: An oligonucleotide composition-based partitioning strategy to aid metagenomic sequence assembly.

Ghosh TS, Mehra V, Mande SS.

J Bioinform Comput Biol. 2015 Jun;13(3):1541004. doi: 10.1142/S0219720015410048. Epub 2015 Feb 8.

PMID:
25790784
6.

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.

7.
8.

Bambus 2: scaffolding metagenomes.

Koren S, Treangen TJ, Pop M.

Bioinformatics. 2011 Nov 1;27(21):2964-71. doi: 10.1093/bioinformatics/btr520. Epub 2011 Sep 16.

9.

Recovering complete and draft population genomes from metagenome datasets.

Sangwan N, Xia F, Gilbert JA.

Microbiome. 2016 Mar 8;4:8. doi: 10.1186/s40168-016-0154-5. Review.

10.

ICoVeR - an interactive visualization tool for verification and refinement of metagenomic bins.

Broeksema B, Calusinska M, McGee F, Winter K, Bongiovanni F, Goux X, Wilmes P, Delfosse P, Ghoniem M.

BMC Bioinformatics. 2017 May 2;18(1):233. doi: 10.1186/s12859-017-1653-5.

11.
12.

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
13.

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.

14.

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets.

Wu YW, Simmons BA, Singer SW.

Bioinformatics. 2016 Feb 15;32(4):605-7. doi: 10.1093/bioinformatics/btv638. Epub 2015 Oct 29.

PMID:
26515820
15.

Revealing large metagenomic regions through long DNA fragment hybridization capture.

Gasc C, Peyret P.

Microbiome. 2017 Mar 14;5(1):33. doi: 10.1186/s40168-017-0251-0.

16.

Fast identification and removal of sequence contamination from genomic and metagenomic datasets.

Schmieder R, Edwards R.

PLoS One. 2011 Mar 9;6(3):e17288. doi: 10.1371/journal.pone.0017288.

17.

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.

18.

Evaluation of viral genome assembly and diversity estimation in deep metagenomes.

Aguirre de Cárcer D, Angly FE, Alcamí A.

BMC Genomics. 2014 Nov 18;15:989. doi: 10.1186/1471-2164-15-989.

19.

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
20.

De novo assembly of bacterial transcriptomes from RNA-seq data.

Tjaden B.

Genome Biol. 2015 Jan 13;16:1. doi: 10.1186/s13059-014-0572-2.

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