GAML: Genome assembly by maximum likelihood

3Citations
Citations of this article
28Readers
Mendeley users who have this article in their library.

This artice is free to access.

Abstract

Background: Resolution of repeats and scaffolding of shorter contigs are critical parts of genome assembly. Modern assemblers usually perform such steps by heuristics, often tailored to a particular technology for producing paired or long reads. Results: We propose a new framework that allows systematic combination of diverse sequencing datasets into a single assembly. We achieve this by searching for an assembly with the maximum likelihood in a probabilistic model capturing error rate, insert lengths, and other characteristics of the sequencing technology used to produce each dataset. We have implemented a prototype genome assembler GAML that can use any combination of insert sizes with Illumina or 454 reads, as well as PacBio reads. Our experiments show that we can assemble short genomes with N50 sizes and error rates comparable to ALLPATHS-LG or Cerulean. While ALLPATHS-LG and Cerulean require each a specific combination of datasets, GAML works on any combination. Conclusions: We have introduced a new probabilistic approach to genome assembly and demonstrated that this approach can lead to superior results when used to combine diverse set of datasets from different sequencing technologies.

Cite

CITATION STYLE

APA

Boža, V., Brejová, B., & Vinař, T. (2015). GAML: Genome assembly by maximum likelihood. Algorithms for Molecular Biology, 10(1). https://doi.org/10.1186/s13015-015-0052-6

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Save time finding and organizing research with Mendeley

Sign up for free