VizBin - An application for reference-independent visualization and human-augmented binning of metagenomic data

Microbiome

Volumn 3, Issue 1, 2015, Pages

  Laczny, Cedric C ^a   Sternal, Tomasz ^b   Plugaru, Valentin ^a   Gawron, Piotr ^a   Atashpendar, Arash ^a   Margossian, Houry H ^a   Coronado, Sergio ^a   der Maaten, Laurens V ^c   Vlassis, Nikos ^d   Wilmes, Paul ^a  

^a UNIVERSITY OF LUXEMBOURG   (Luxembourg)

^b POZNAN UNIVERSITY OF TECHNOLOGY   (Poland)

^c DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

^d ADOBE RESEARCH   (United States)

Author keywords

Binning; Machine learning; Metagenomics; Visualization

Indexed keywords

ARTICLE; COMPUTER INTERFACE; DATA ANALYSIS SOFTWARE; GENOME; INFORMATION PROCESSING; MAXBIN; METAGENOMICS; MICROBIAL COMMUNITY; MICROBIAL CONSORTIUM; PATTERN RECOGNITION; PRIORITY JOURNAL; VIZBIN;

MALUS X DOMESTICA;

EID: 84938483160     PISSN: None     EISSN: 20492618     Source Type: Journal    
DOI: 10.1186/s40168-014-0066-1     Document Type: Article

References (24)

1. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004, 304(5667):66-74. doi:10.1126/science.1093857, 10.1126/science.1093857, 15001713.
2. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 2004, 428(6978):37-43. doi:10.1038/nature02340, 10.1038/nature02340, 14961025.
3. Warnecke F, Luginbühl P, Ivanova N, Ghassemian M, Richardson TH, Stege JT, et al. Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature 2007, 450(7169):560-5. doi:10.1038/nature06269, 10.1038/nature06269, 18033299.
4. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010, 464(7285):59-65. doi:10.1038/nature08821, 10.1038/nature08821, 20203603.
5. Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR,. Enterotypes of the human gut microbiome. Nature 2011, 473(7346):174-80. doi:10.1038/nature09944, 10.1038/nature09944, 21508958.
6. Howe AC, Jansson JK, Malfatti SA, Tringe SG, Tiedje JM, Brown CT. Tackling soil diversity with the assembly of large, complex metagenomes. Proc Natl Acad Sci USA. 2014, 111(13):4904-9. doi:10.1073/pnas.1402564111, 10.1073/pnas.1402564111, 24632729.
7. Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, Berger S, Kultima JR, et al. Metagenomic species profiling using universal phylogenetic marker genes. Nat Methods. 2013, 10(12):1196-9. doi:10.1038/nmeth.2693, 10.1038/nmeth.2693, 24141494.
8. Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 2014, 15(3):46. doi:10.1186/gb-2014-15-3-r46, 10.1186/gb-2014-15-3-r46.
9. Wilmes P, Simmons SL, Denef VJ, Banfield JF. The dynamic genetic repertoire of microbial communities. FEMS Microbiol Rev. 2009, 33(1):109-32. doi:10.1111/j.1574-6976.2008.00144.x, 10.1111/j.1574-6976.2008.00144.x, 19054116.
10. Karlin S, Burge C. Dinucleotide relative abundance extremes: a genomic signature. Trends Genet. 1995, 11(7):283-90. 10.1016/S0168-9525(00)89076-9, 7482779.
11. Gori F, Mavroedis D, Jetten MSM, Marchiori E. Genomic signatures for metagenomic data analysis: exploiting the reverse complementarity of tetranucleotides. 2011 IEEE Int Conf Systems Biol (ISB) 2011, IEEE, Zhuhai, China, Chen L, Zhang X-S, Wu L-Y, Wang Y, doi:10.1109/ISB.2011.6033147.
12. Abe T, Kanaya S, Kinouchi M, Ichiba Y, Kozuki T, Ikemura T. Informatics for unveiling hidden genome signatures. Genome Res. 2003, 13(4):693-702. doi:10.1101/gr.634603, 10.1101/gr.634603, 12671005.
13. Dick GJ, Andersson AF, Baker BJ, Simmons SL, Thomas BC, Yelton A. Community-wide analysis of microbial genome sequence signatures. Genome Biol. 2009, 10(8):85. doi:10.1186/gb-2009-10-8-r85, 10.1186/gb-2009-10-8-r85.
14. Laczny CC, Pinel N, Vlassis N, Wilmes P. Alignment-free visualization of metagenomic data by nonlinear dimension reduction. Sci Rep. 2014, 4:4516. doi:10.1038/srep04516, 10.1038/srep04516, 24682077.
15. Van Der Maaten L, Barnes-Hut-SNE. arXiv. 2013:1301-33421.
16. Wu Y-W, Tang Y-H, Tringe SG, Simmons BA, Singer SW. MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome 2014, 2(1):26. doi:10.1186/2049-2618-2-26, 10.1186/2049-2618-2-26, 25136443.
17. Dupont CL, Rusch DB, Yooseph S, Lombardo M-J, Richter RA, Valas R,. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. ISME J 2012, 6(6):1186-99. doi:10.1038/ismej.2011.189, 10.1038/ismej.2011.189, 22170421.
18. Albertsen M, Hugenholtz P, Skarshewski A, Nielsen K, Tyson GW, Nielsen PH. Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol. 2013, 31(6):533-8. doi:10.1038/nbt.2579, 10.1038/nbt.2579, 23707974.
19. Structure, function and diversity of the healthy human microbiome. Nature 2012, 486(7402):207-14. doi:10.1038/nature11234, 10.1038/nature11234.
20. Wrighton KC, Thomas BC, Sharon I, Miller CS, Castelle CJ, VerBerkmoes NC, et al. Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science 2012, 337(6102):1661-5. doi:10.1126/science.1224041, 10.1126/science.1224041, 23019650.
21. Strous M, Kraft B, Bisdorf R, Tegetmeyer HE. The binning of metagenomic contigs for microbial physiology of mixed cultures. Front Microbiol 2012, 3:410. doi:10.3389/fmicb.2012.00410, 10.3389/fmicb.2012.00410, 23227024.
22. Imelfort M, Parks D, Woodcroft BJ, Dennis P, Hugenholtz P, Tyson GW. GroopM: an automated tool for the recovery of population genomes from related metagenomes. PeerJ 2014, 2:603. doi:10.7717/peerj.603, 10.7717/peerj.603.
23. Nielsen HB, Almeida M, Juncker AS, Rasmussen S, Li J, Sunagawa S,. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes. Nat Biotechnol 2014, 32(8):822-8. doi:10.1038/nbt.2939, 10.1038/nbt.2939, 24997787.
24. Alneberg J, Bjarnason BS, de Bruijn I, Schirmer M, Quick J, Ijaz UZ, et al. Binning metagenomic contigs by coverage and composition. Nat Methods. 2014. doi:10.1038/nmeth.3103.