title: Integrating genome assemblies with MAIA.
abstract: 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.
authors.affiliation: Department of Mediamatics, Delft University of Technology, Delft, The Netherlands. j.f.nijkamp@tudelft.nl
authors.forename: Jurgen
authors.initials: J
authors.lastname: Nijkamp
authors.forename: Wynand
authors.initials: W
authors.lastname: Winterbach
authors.forename: Marcel
authors.initials: M
authors.lastname: van den Broek
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Daran
authors.forename: Marcel
authors.initials: M
authors.lastname: Reinders
authors.forename: Dick
authors.initials: D
authors.lastname: de Ridder
mesh_terms: 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
chemical_list: D004271:DNA, Fungal
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