Integrating genome assemblies with MAIA

Motivation: De novo assembly of a eukaryotic genome with NGS 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, i.e. multiple de novo assemblies and mappings against multiple related genomes, by optimizing a weighted set 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 to the single assemblies. Availability: MAIA is availabe as a Matlab package and can be downloaded from http://bioinformatics.tudelft.nl.