De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii
نویسندگان
چکیده
منابع مشابه
De novo assembly of short sequence reads
A new generation of sequencing technologies is revolutionizing molecular biology. Illumina's Solexa and Applied Biosystems' SOLiD generate gigabases of nucleotide sequence per week. However, a perceived limitation of these ultra-high-throughput technologies is their short read-lengths. De novo assembly of sequence reads generated by classical Sanger capillary sequencing is a mature field of res...
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Although many de novo genome assembly projects have recently been conducted using high-throughput sequencers, assembling highly heterozygous diploid genomes is a substantial challenge due to the increased complexity of the de Bruijn graph structure predominantly used. To address the increasing demand for sequencing of nonmodel and/or wild-type samples, in most cases inbred lines or fosmid-based...
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Repeat elements are important components of eukaryotic genomes. One limitation in our understanding of repeat elements is that most analyses rely on reference genomes that are incomplete and often contain missing data in highly repetitive regions that are difficult to assemble. To overcome this problem we develop a new method, REPdenovo, which assembles repeat sequences directly from raw shotgu...
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The assembly of long reads from Pacific Biosciences and Oxford Nanopore Technologies typically requires resource-intensive error-correction and consensus-generation steps to obtain high-quality assemblies. We show that the error-correction step can be omitted and that high-quality consensus sequences can be generated efficiently with a SIMD-accelerated, partial-order alignment-based, stand-alon...
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ژورنال
عنوان ژورنال: BMC Genomics
سال: 2017
ISSN: 1471-2164
DOI: 10.1186/s12864-017-4165-9