MOTIVATION: Novel high-throughput sequencing technologies pose new algorithmic challenges in handling massive amounts of short-read, high-coverage data. A robust and versatile consensus tool is of particular interest for such data since a sound multi-read alignment is a prerequisite for variation analyses, accurate genome assemblies and insert sequencing. RESULTS: A multi-read alignment algorithm for de novo or reference-guided genome assembly is presented. The program identifies segments shared by multiple reads and then aligns these segments using a consistency-enhanced alignment graph. On real de novo sequencing data obtained from the newly established NCBI Short Read Archive, the program performs similarly in quality to other comparable programs. On more challenging simulated datasets for insert sequencing and variation analyses, our program outperforms the other tools. AVAILABILITY: The consensus program can be downloaded from http://www.seqan.de/projects/consensus.html. It can be used stand-alone or in conjunction with the Celera Assembler. Both application scenarios as well as the usage of the tool are described in the documentation.
MOTIVATION: Novel high-throughput sequencing technologies pose new algorithmic challenges in handling massive amounts of short-read, high-coverage data. A robust and versatile consensus tool is of particular interest for such data since a sound multi-read alignment is a prerequisite for variation analyses, accurate genome assemblies and insert sequencing. RESULTS: A multi-read alignment algorithm for de novo or reference-guided genome assembly is presented. The program identifies segments shared by multiple reads and then aligns these segments using a consistency-enhanced alignment graph. On real de novo sequencing data obtained from the newly established NCBI Short Read Archive, the program performs similarly in quality to other comparable programs. On more challenging simulated datasets for insert sequencing and variation analyses, our program outperforms the other tools. AVAILABILITY: The consensus program can be downloaded from http://www.seqan.de/projects/consensus.html. It can be used stand-alone or in conjunction with the Celera Assembler. Both application scenarios as well as the usage of the tool are described in the documentation.
Authors: Paul Havlak; Rui Chen; K James Durbin; Amy Egan; Yanru Ren; Xing-Zhi Song; George M Weinstock; Richard A Gibbs Journal: Genome Res Date: 2004-04 Impact factor: 9.043
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: Serafim Batzoglou; David B Jaffe; Ken Stanley; Jonathan Butler; Sante Gnerre; Evan Mauceli; Bonnie Berger; Jill P Mesirov; Eric S Lander Journal: Genome Res Date: 2002-01 Impact factor: 9.043
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: Chen-Shan Chin; David H Alexander; Patrick Marks; Aaron A Klammer; James Drake; Cheryl Heiner; Alicia Clum; Alex Copeland; John Huddleston; Evan E Eichler; Stephen W Turner; Jonas Korlach Journal: Nat Methods Date: 2013-05-05 Impact factor: 28.547
Authors: Juliane D Klein; Stephan Ossowski; Korbinian Schneeberger; Detlef Weigel; Daniel H Huson Journal: PLoS One Date: 2011-08-15 Impact factor: 3.240
Authors: Andres Benavides; Juan Pablo Isaza; Juan Pablo Niño-García; Juan Fernando Alzate; Felipe Cabarcas Journal: BMC Genomics Date: 2018-12-11 Impact factor: 3.969
Authors: Sean R Landman; Tae Hyun Hwang; Kevin A T Silverstein; Yingming Li; Scott M Dehm; Michael Steinbach; Vipin Kumar Journal: BMC Genomics Date: 2014-01-29 Impact factor: 3.969