A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads.
BACKGROUND
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.


BACKGROUND
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.
Rausch
Tobias
T
International Max Planck Research School for Computational Biology and Scientific Computing, Ihnestr. 63-73, Algorithmische Bioinformatik, Institut für Informatik, Takustr. 9, 14195 Berlin, Germany. rausch@inf.fu-berlin.de
Koren
Sergey
S
Denisov
Gennady
G
Weese
David
D
Emde
Anne-Katrin
AK
Döring
Andreas
A
Reinert
Knut
K
D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D020407:Internet; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods