title: MBBC: an efficient approach for metagenomic binning based on clustering.
abstract: BACKGROUND
  Binning environmental shotgun reads is one of the most fundamental tasks in metagenomic studies, in which mixed reads from different species or operational taxonomical units (OTUs) are separated into different groups. While dozens of binning methods are available, there is still room for improvement.
  
  
  RESULTS
  We developed a novel taxonomy-independent approach called MBBC (Metagenomic Binning Based on Clustering) to cluster environmental shotgun reads, by considering k-mer frequency in reads and Markov properties of the inferred OTUs. Tested on twelve simulated datasets, MBBC reliably estimated the species number, the genome size, and the relative abundance of each species, independent of whether there are errors in reads. Tested on multiple experimental datasets, MBBC outperformed two state-of-the-art taxonomy-independent methods, in terms of the accuracy of the estimated species number, genome sizes, and percentages of correctly assigned reads, among other metrics.
  
  
  CONCLUSIONS
  We have developed a novel method for binning metagenomic reads based on clustering. This method is demonstrated to reliably predict species numbers, genome sizes, relative species abundances, and k-mer coverage in simple datasets. Our method also has a high accuracy in read binning. The MBBC software is freely available at http://eecs.ucf.edu/~xiaoman/MBBC/MBBC.html .
authors: Department of Electric Engineering and Computer Science, University of Central Florida, Orlando, FL, 32816, USA. ying2010@knights.ucf.edu.
authors: Ying
authors: Y
authors: Wang
authors: Department of Electric Engineering and Computer Science, University of Central Florida, Orlando, FL, 32816, USA. haihu@cs.ucf.edu.
authors: Haiyan
authors: H
authors: Hu
authors: Department of Electric Engineering and Computer Science, University of Central Florida, Orlando, FL, 32816, USA. xiaoman@mail.ucf.edu.|Burnett School of Biomedical Science, University of Central Florida, Orlando, FL, 32816, USA. xiaoman@mail.ucf.edu.
authors: Xiaoman
authors: X
authors: Li
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D008390:Markov Chains; D056186:Metagenomics; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
references: Genome Res. 2003 Feb;13(2):145-58
references: 12566393
references: Science. 2004 Apr 2;304(5667):66-74
references: 15001713
references: PLoS Biol. 2007 Mar;5(3):e82
references: 17355177
references: Bioinformatics. 2008 Feb 15;24(4):462-7
references: 18202027
references: BMC Bioinformatics. 2009 Feb 11;10:56
references: 19210774
references: BMC Bioinformatics. 2009 Dec 18;10:430
references: 20021646
references: Nucleic Acids Res. 2008 Apr;36(7):2230-9
references: 18285365
references: Genome Res. 2007 Mar;17(3):377-86
references: 17255551
references: BMC Genomics. 2010 Aug 05;11:461
references: 20687950
references: Bioinformatics. 2011 Jun 1;27(11):1489-95
references: 21493653
references: Brief Bioinform. 2012 Nov;13(6):669-81
references: 22962338
references: Genome Res. 2003 Aug;13(8):1916-22
references: 12902383
references: Bioinformatics. 2010 Apr 1;26(7):960-1
references: 20172941
references: Stand Genomic Sci. 2011 Nov 30;5(2):248-53
references: 22180827
references: BMC Bioinformatics. 2010 Oct 15;11 Suppl 7:S14
references: 21106121
references: Bioinformatics. 2006 Sep 15;22(18):2210-6
references: 16809387
references: Proc Natl Acad Sci U S A. 1998 Aug 18;95(17):10026-31
references: 9707594
references: Nucleic Acids Res. 1998 Jan 15;26(2):544-8
references: 9421513
references: Nature. 2004 Mar 4;428(6978):37-43
references: 14961025
references: BMC Bioinformatics. 2010 Apr 16;11 Suppl 2:S5
references: 20406503
references: BMC Bioinformatics. 2008 Sep 19;9:386
references: 18803844
references: Bioinformatics. 2010 Feb 15;26(4):568-9
references: 20007739
references: Adv Bioinformatics. 2008;2008:205969
references: 19956701
references: Bioinformatics. 2009 Aug 1;25(15):1966-7
references: 19497933
references: Bioinformatics. 2012 Sep 15;28(18):i356-i362
references: 22962452
references: Annu Rev Genet. 2004;38:771-92
references: 15568993
references: Bioinformatics. 2009 Jul 15;25(14):1722-30
references: 19439565
references: Brief Bioinform. 2012 Nov;13(6):728-42
references: 22966151
references: Environ Microbiol. 2004 Sep;6(9):938-47
references: 15305919
references: Genome Biol. 2008 Oct 13;9(10):R151
references: 18851752
references: Nat Methods. 2009 Sep;6(9):673-6
references: 19648916
references: BMC Bioinformatics. 2008 Apr 28;9:215
references: 18442374
references: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D115-9
references: 14681372
references: J Comput Biol. 2011 Mar;18(3):523-34
references: 21385052
references: Curr Protoc Bioinformatics. 2003 Feb;Chapter 10:Unit 10.3
references: 18428693
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D290-301
references: 22127870
references: Nat Methods. 2011 Mar;8(3):191-2
references: 21358620
references: Nat Methods. 2007 Jan;4(1):63-72
references: 17179938
references: BMC Bioinformatics. 2010 Oct 30;11:538
references: 21034504
references: PLoS One. 2008 Oct 08;3(10):e3373
references: 18841204