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Exploring genome characteristics and sequence quality without a reference.

ABSTRACT: The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to assisting the user with the assembly.This article addresses the practical aspects of de novo assembly by introducing new ways to perform quality assessment on a collection of sequence reads. The software implementation calculates per-base error rates, paired-end fragment-size distributions and coverage metrics in the absence of a reference genome. Additionally, the software will estimate characteristics of the sequenced genome, such as repeat content and heterozygosity that are key determinants of assembly difficulty.

SUBMITTER: Simpson JT

PROVIDER: S-EPMC3998141 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature

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Exploring genome characteristics and sequence quality without a reference.

Simpson Jared T JT

Bioinformatics (Oxford, England) 20140117 9

<h4>Motivation</h4>The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to assisting the user with the assembly.<h4>Results</h4>This article addresses the practical aspects of de novo assembly by introducing new ways to perform quality assessment on a collection of sequence reads. The software implementation calculates ...[more]

PMID: 24443382

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Project description:Genomics research in mammals has produced reference genome sequences that are essential for identifying variation associated with disease. High quality reference genome sequences are now available for humans, model species, and economically important agricultural animals. Comparisons between these species have provided unique insights into mammalian gene function. However, the number of species with reference genomes is small compared to those needed for studying molecular evolutionary relationships in the tree of life. For example, among the even-toed ungulates there are approximately 300 species whose phylogenetic relationships have been calculated in the 10k trees project. Only six of these have reference genomes: cattle, swine, sheep, goat, water buffalo, and bison. Although reference sequences will eventually be developed for additional hoof stock, the resources in terms of time, money, infrastructure and expertise required to develop a quality reference genome may be unattainable for most species for at least another decade. In this work we mapped 35 Gb of next generation sequence data of a Katahdin sheep to its own species' reference genome ( Ovis aries Oar3.1) and to that of a species that diverged 15 to 30 million years ago ( Bos taurus UMD3.1). In total, 56% of reads covered 76% of UMD3.1 to an average depth of 6.8 reads per site, 83 million variants were identified, of which 78 million were homozygous and likely represent interspecies nucleotide differences. Excluding repeat regions and sex chromosomes, nearly 3.7 million heterozygous sites were identified in this animal vs. bovine UMD3.1, representing polymorphisms occurring in sheep. Of these, 41% could be readily mapped to orthologous positions in ovine Oar3.1 with 80% corroborated as heterozygous. These variant sites, identified via interspecies mapping could be used for comparative genomics, disease association studies, and ultimately to understand mammalian gene function.

Dataset Information

Exploring genome characteristics and sequence quality without a reference.

Publications

Exploring genome characteristics and sequence quality without a reference.

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