Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs
نویسندگان
چکیده
منابع مشابه
Accurate self-correction of errors in long reads using de Bruijn graphs
Motivation New long read sequencing technologies, like PacBio SMRT and Oxford NanoPore, can produce sequencing reads up to 50 000 bp long but with an error rate of at least 15%. Reducing the error rate is necessary for subsequent utilization of the reads in, e.g. de novo genome assembly. The error correction problem has been tackled either by aligning the long reads against each other or by a h...
متن کاملToward perfect reads
We propose a new method to correct short reads using de Bruijn graphs, and implement it as a tool called Bcool. As a first step, Bcool constructs a corrected compacted de Bruijn graph from the reads. This graph is then used as a reference and the reads are corrected according to their mapping on the graph. We show that this approach yields a better correction than kmer-spectrum techniques, whil...
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The recent breakthroughs in assembling long error-prone reads were based on the overlap-layout-consensus (OLC) approach and did not utilize the strengths of the alternative de Bruijn graph approach to genome assembly. Moreover, these studies often assume that applications of the de Bruijn graph approach are limited to short and accurate reads and that the OLC approach is the only practical para...
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MOTIVATION Second generation sequencing technologies paved the way to an exceptional increase in the number of sequenced genomes, both prokaryotic and eukaryotic. However, short reads are difficult to assemble and often lead to highly fragmented assemblies. The recent developments in long reads sequencing methods offer a promising way to address this issue. However, so far long reads are charac...
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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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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2019
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btz102