May 3, 2016

trio-sga: facilitating de novo assembly of highly heterozygous genomes with parent-child trios

BioRxiv : the Preprint Server for Biology
Milan MalinskyRichard Durbin

Abstract

Motivation: Most DNA sequence in diploid organisms is found in two copies, one contributed by the mother and the other by the father. The high density of differences between the maternally and paternally contributed sequences (heterozygous sites) in some organisms makes de novo genome assembly very challenging, even for algorithms specifically designed to deal with these cases. Therefore, various approaches, most commonly inbreeding in the laboratory, are used to reduce heterozygosity in genomic data prior to assembly. However, many species are not amenable to these techniques. Results: We introduce trio-sga, a set of three algorithms designed to take advantage of mother-father-offspring trio sequencing to facilitate better quality genome assembly in organisms with moderate to high levels of heterozygosity. Two of the algorithms use haplotype phase information present in the trio data to eliminate the majority of heterozygous sites before the assembly commences. The third algorithm is designed to reduce sequencing costs by enabling the use of parents' reads in the assembly of the genome of the offspring. We test these algorithms on a 'simulated trio' from four haploid datasets, and further demonstrate their performance by assem...Continue Reading

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Mentioned in this Paper

Supramarginal Gyrus, Anterior Division (SGa)
Genome
Genome Assembly Sequence
Laboratory
Cocaine
Haploid Cell
Site
Genomics
Sequencing
Simulation

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