Abstract
The ordering and orientation of genomic scaffolds to reconstruct chromosomes is an essential step during de novo genome assembly. Because this process utilizes various mapping techniques that each provides an independent line of evidence, a combination of multiple maps can improve the accuracy of the resulting chromosomal assemblies. We present ALLMAPS, a method capable of computing a scaffold ordering that maximizes colinearity across a collection of maps. ALLMAPS is robust against common mapping errors, and generates sequences that are maximally concordant with the input maps. ALLMAPS is a useful tool in building high-quality genome assemblies. ALLMAPS is available at: https://github.com/tanghaibao/jcvi/wiki/ALLMAPS.
Highlights
A hierarchical approach is typically adopted for the assembly of large eukaryotic genomes - starting with identifying overlapping reads to build contigs, adding paired reads to build scaffolds, and ordering and orientating scaffolds together to assemble chromosomes using various sources of long distance information [1,2]
In the ALLMAPS implementation, we chose to use Genetic Algorithm (GA) instead of some other heuristics such as local search, hill climbing, and greedy strategy to avoid getting stuck in local optima [25,26]
ALLMAPS anchored 384 Mb of scaffold sequences onto the eight chromosomes, more than the anchor rate based on any single map alone, and matched the anchor rate in the published Mt4.0 assembly that is a product of intensive manual curation [8]
Summary
A hierarchical approach is typically adopted for the assembly of large eukaryotic genomes - starting with identifying overlapping reads to build contigs, adding paired reads to build scaffolds, and ordering and orientating scaffolds together to assemble chromosomes using various sources of long distance information [1,2]. During this hierarchical process, larger and larger sequence chunks are assembled and ‘anchored’ onto chromosomal-sized pieces. While initially designed to use genetic maps to guide the chromosomal anchoring process and produce a close-to-optimal scaffold configuration, ALLMAPS can utilize a variety of techniques for generating physical and comparative maps of chromosomes
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