Integrating genome assemblies with MAIA.
BACKGROUND
De novo assembly of a eukaryotic genome with next-generation sequencing data is still a challenging task. Over the past few years several assemblers have been developed, often suitable for one specific type of sequencing data. The number of known genomes is expanding rapidly, therefore it becomes possible to use multiple reference genomes for assembly projects. We introduce an assembly integrator that makes use of all available data, i.e. multiple de novo assemblies and mappings against multiple related genomes, by optimizing a weighted combination of criteria.


RESULTS
The developed algorithm was applied on the de novo sequencing of the Saccharomyces cerevisiae CEN.PK 113-7D strain. Using Solexa and 454 read data, two de novo and three comparative assemblies were constructed and subsequently integrated, yielding 29 contigs, covering more than 12 Mbp; a drastic improvement compared with the single assemblies.


BACKGROUND
MAIA is available as a Matlab package and can be downloaded from http://bioinformatics.tudelft.nl.
Nijkamp
Jurgen
J
Department of Mediamatics, Delft University of Technology, Delft, The Netherlands. j.f.nijkamp@tudelft.nl
Winterbach
Wynand
W
van den Broek
Marcel
M
Daran
Jean-Marc
JM
Reinders
Marcel
M
de Ridder
Dick
D
D000465:Algorithms; D003196:Computer Graphics; D020451:Contig Mapping; D004271:DNA, Fungal; D016681:Genome, Fungal; D023281:Genomics / Q000379:methods*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D017422:Sequence Analysis, DNA
D004271:DNA, Fungal
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