MOTIVATION: Sequencing projects increasingly target samples from non-clonal sources. In particular, metagenomics has enabled scientists to begin to characterize the structure of microbial communities. The software tools developed for assembling and analyzing sequencing data for clonal organisms are, however, unable to adequately process data derived from non-clonal sources. RESULTS: We present a new scaffolder, Bambus 2, to address some of the challenges encountered when analyzing metagenomes. Our approach relies on a combination of a novel method for detecting genomic repeats and algorithms that analyze assembly graphs to identify biologically meaningful genomic variants. We compare our software to current assemblers using simulated and real data. We demonstrate that the repeat detection algorithms have higher sensitivity than current approaches without sacrificing specificity. In metagenomic datasets, the scaffolder avoids false joins between distantly related organisms while obtaining long-range contiguity. Bambus 2 represents a first step toward automated metagenomic assembly. AVAILABILITY: Bambus 2 is open source and available from http://amos.sf.net. CONTACT: mpop@umiacs.umd.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: Sequencing projects increasingly target samples from non-clonal sources. In particular, metagenomics has enabled scientists to begin to characterize the structure of microbial communities. The software tools developed for assembling and analyzing sequencing data for clonal organisms are, however, unable to adequately process data derived from non-clonal sources. RESULTS: We present a new scaffolder, Bambus 2, to address some of the challenges encountered when analyzing metagenomes. Our approach relies on a combination of a novel method for detecting genomic repeats and algorithms that analyze assembly graphs to identify biologically meaningful genomic variants. We compare our software to current assemblers using simulated and real data. We demonstrate that the repeat detection algorithms have higher sensitivity than current approaches without sacrificing specificity. In metagenomic datasets, the scaffolder avoids false joins between distantly related organisms while obtaining long-range contiguity. Bambus 2 represents a first step toward automated metagenomic assembly. AVAILABILITY: Bambus 2 is open source and available from http://amos.sf.net. CONTACT: mpop@umiacs.umd.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Gene W Tyson; Jarrod Chapman; Philip Hugenholtz; Eric E Allen; Rachna J Ram; Paul M Richardson; Victor V Solovyev; Edward M Rubin; Daniel S Rokhsar; Jillian F Banfield Journal: Nature Date: 2004-02-01 Impact factor: 49.962
Authors: E W Myers; G G Sutton; A L Delcher; I M Dew; D P Fasulo; M J Flanigan; S A Kravitz; C M Mobarry; K H Reinert; K A Remington; E L Anson; R A Bolanos; H H Chou; C M Jordan; A L Halpern; S Lonardi; E M Beasley; R C Brandon; L Chen; P J Dunn; Z Lai; Y Liang; D R Nusskern; M Zhan; Q Zhang; X Zheng; G M Rubin; M D Adams; J C Venter Journal: Science Date: 2000-03-24 Impact factor: 47.728
Authors: N T Perna; G Plunkett; V Burland; B Mau; J D Glasner; D J Rose; G F Mayhew; P S Evans; J Gregor; H A Kirkpatrick; G Pósfai; J Hackett; S Klink; A Boutin; Y Shao; L Miller; E J Grotbeck; N W Davis; A Lim; E T Dimalanta; K D Potamousis; J Apodaca; T S Anantharaman; J Lin; G Yen; D C Schwartz; R A Welch; F R Blattner Journal: Nature Date: 2001-01-25 Impact factor: 49.962
Authors: Stefan Kurtz; Adam Phillippy; Arthur L Delcher; Michael Smoot; Martin Shumway; Corina Antonescu; Steven L Salzberg Journal: Genome Biol Date: 2004-01-30 Impact factor: 13.583
Authors: Steven L Salzberg; Adam M Phillippy; Aleksey Zimin; Daniela Puiu; Tanja Magoc; Sergey Koren; Todd J Treangen; Michael C Schatz; Arthur L Delcher; Michael Roberts; Guillaume Marçais; Mihai Pop; James A Yorke Journal: Genome Res Date: 2012-01-06 Impact factor: 9.043
Authors: Aleksey V Zimin; Guillaume Marçais; Daniela Puiu; Michael Roberts; Steven L Salzberg; James A Yorke Journal: Bioinformatics Date: 2013-08-29 Impact factor: 6.937
Authors: Migun Shakya; Christopher Quince; James H Campbell; Zamin K Yang; Christopher W Schadt; Mircea Podar Journal: Environ Microbiol Date: 2013-02-06 Impact factor: 5.491
Authors: Todd J Treangen; Sergey Koren; Daniel D Sommer; Bo Liu; Irina Astrovskaya; Brian Ondov; Aaron E Darling; Adam M Phillippy; Mihai Pop Journal: Genome Biol Date: 2013-01-15 Impact factor: 13.583