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

Bioinformatics

Volumn 32, Issue 4, 2016, Pages 605-607

  Wu, Yu Wei ^a,b   Simmons, Blake A ^a,b,c   Singer, Steven W ^a,b  

^a JOINT BIOENERGY INSTITUTE   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c SANDIA NATIONAL LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BACTERIAL GENOME; METAGENOME; METAGENOMICS; MICROBIAL GENOME; PROCEDURES; SOFTWARE;

ALGORITHMS; GENOME, BACTERIAL; GENOME, MICROBIAL; METAGENOME; METAGENOMICS; SOFTWARE;

EID: 84957911451     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv638     Document Type: Article

References (14)

1. Albertsen, M. et al (2013) Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat. Biotechnol., 31, 533-538.
2. Alneberg, J. et al (2014) Binning metagenomic contigs by coverage and composition. Nat. Methods, 11, 1144-1146.
3. Dick, G. J. et al. (2009) Community-wide analysis of microbial genome sequence signatures. Genome Biol., 10, R85.
4. Imelfort, M. et al. (2014) GroopM: an automated tool for the recovery of population genomes from related metagenomes. PeerJ, 2, e603.
5. Iverson, V. et al. (2012) Untangling genomes from metagenomes: revealing an uncultured class of marine Euryarchaeota. Science, 335, 587-590.
6. Li, D. et al. (2015) MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics, 31, 1674-1676.
7. Kang, D. D. et al. (2015) MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3, e1165.
8. Mackelprang, R. et al. (2011) Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature, 480, 368-371.
9. Richter, Y. et al. (2008) MetaSim: a sequencing simulator for genomics and metagenomics. PLoS One, 3, e3373.
10. Sharon, I. et al. (2013) Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Res., 23, 111-120.
11. Wang, Y. et al. (2012) MetaCluster 5. 0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample. Bioinformatics, 28, i356-i362.
12. Wrighton, K. C. et al. (2012) Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science, 337, 1661-1665.
13. Wu, Y. W. and Ye, Y. (2011) A novel abundance-based algorithm for binning metagenomic sequences using l-tuples. J. Comput. Biol., 18, 523-534.
14. Wu, Y. W. et al. (2014) MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome, 2, 26.