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.
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     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 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:},
     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 = {},
     volume = {25},
     year = {2009}
  • T. Rausch, A.-K. Emde, K. Reinert, “Robust consensus computation”, vol. 9, iss. Suppl 10, 2008.
    cite this publication
     author = {T. Rausch and A.-K. Emde and K. Reinert},
     journal = {BMC Bioinformatics},
     number = {Suppl 10},
     pages = {P4},
     title = {Robust consensus computation},
     url = {},
     volume = {9},
     year = {2008}


For questions, comments, or suggestions please contact:

Tobias Rausch