SeqCons2

Abstract

Sequence consensus 2 is an open source consensus computation program for Linux and Windows. The algorithm can be used for de novo and reference-guided sequence assembly.

Please Cite

T. Rausch, S. Koren, G. Denisov, D. Weese, A.-K. Emde, A. Döring, K. Reinert, “A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads”, vol. 25, iss. 9, 2009.

cite this publication

@article{fu_mi_publications392,
 abstract = {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. Contact: rausch@inf.fu-berlin.de},
 author = {T. Rausch and S. Koren and G. Denisov and D. Weese and A.-K. Emde and A. D{\"o}ring and
  K. Reinert},
 journal = {Bioinformatics},
 number = {9},
 pages = {1118--1124},
 publisher = {Oxford University Press},
 title = {A consistency-based consensus algorithm for de novo and reference-guided sequence assembly
  of short reads},
 url = {http://publications.imp.fu-berlin.de/392/},
 volume = {25},
 year = {2009}
}

T. Rausch, A.-K. Emde, K. Reinert, “Robust consensus computation”, vol. 9, iss. Suppl 10, 2008.

cite this publication

@article{fu_mi_publications390,
 author = {T. Rausch and A.-K. Emde and K. Reinert},
 journal = {BMC Bioinformatics},
 number = {Suppl 10},
 pages = {P4},
 title = {Robust consensus computation},
 url = {http://publications.imp.fu-berlin.de/390/},
 volume = {9},
 year = {2008}
}

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For questions, comments, or suggestions please contact:

Tobias Rausch

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