Platanus_B: an accurate de novo assembler for bacterial genomes using an iterative error-removal process
نویسندگان
چکیده
منابع مشابه
Assembler for de novo assembly of large genomes.
Assembling a large genome using next generation sequencing reads requires large computer memory and a long execution time. To reduce these requirements, we propose an extension-based assembler, called JR-Assembler, where J and R stand for "jumping" extension and read "remapping." First, it uses the read count to select good quality reads as seeds. Second, it extends each seed by a whole-read ex...
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The de Bruijn graph assembly approach breaks reads into k-mers before assembling them into contigs. The string graph approach forms contigs by connecting two reads with k or more overlapping nucleotides. Both approaches must deal with the following problems: false-positive vertices, due to erroneous reads; gap problem, due to non-uniform coverage; branching problem, due to erroneous reads and r...
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MOTIVATION Many de novo genome assemblers have been proposed recently. The basis for most existing methods relies on the de bruijn graph: a complex graph structure that attempts to encompass the entire genome. Such graphs can be prohibitively large, may fail to capture subtle information and is difficult to be parallelized. RESULT We present a method that eschews the traditional graph-based a...
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As whole genome sequencing has become a routine biological experiment, algorithms for assembly of whole genome shotgun data has become a topic of extensive research, with a plethora of off-the-shelf methods that can reconstruct the genomes of many organisms. Simultaneously, several recently sequenced genomes exhibit very high polymorphism rates. For these organisms genome assembly remains a cha...
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RNA sequencing based on next-generation sequencing technology is useful for analyzing transcriptomes, discovering novel genes and studying exon/intron structures. Similar to genome assembly, de novo transcriptome assembly does not rely on a reference genome and additional annotated information. Most, if not all, existing de novo transcriptome assemblers rely heavily on de novo genome assembly t...
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ژورنال
عنوان ژورنال: DNA Research
سال: 2020
ISSN: 1340-2838,1756-1663
DOI: 10.1093/dnares/dsaa014