About: Arapan-S: a fast and highly accurate whole-genome assembly software for viruses and small genomes

Facets (new session)
Description
Metadata
Settings
- owl:sameAs
- Inference Rule:

About: Arapan-S: a fast and highly accurate whole-genome assembly software for viruses and small genomes Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
title	Arapan-S: a fast and highly accurate whole-genome assembly software for viruses and small genomes
Creator	Sahli, Mohammed Shibuya, Tetsuo
source	Medline; PMC
abstract	BACKGROUND: Genome assembly is considered to be a challenging problem in computational biology, and has been studied extensively by many researchers. It is extremely difficult to build a general assembler that is able to reconstruct the original sequence instead of many contigs. However, we believe that creating specific assemblers, for solving specific cases, will be much more fruitful than creating general assemblers. FINDINGS: In this paper, we present Arapan-S, a whole-genome assembly program dedicated to handling small genomes. It provides only one contig (along with the reverse complement of this contig) in many cases. Although genomes consist of a number of segments, the implemented algorithm can detect all the segments, as we demonstrate for Influenza Virus A. The Arapan-S program is based on the de Bruijn graph. We have implemented a very sophisticated and fast method to reconstruct the original sequence and neglect erroneous k-mers. The method explores the graph by using neither the shortest nor the longest path, but rather a specific and reliable path based on the coverage level or k-mers’ lengths. Arapan-S uses short reads, and it was tested on raw data downloaded from the NCBI Trace Archive. CONCLUSIONS: Our findings show that the accuracy of the assembly was very high; the result was checked against the European Bioinformatics Institute (EBI) database using the NCBI BLAST Sequence Similarity Search. The identity and the genome coverage was more than 99%. We also compared the efficiency of Arapan-S with other well-known assemblers. In dealing with small genomes, the accuracy of Arapan-S is significantly higher than the accuracy of other assemblers. The assembly process is very fast and requires only a few seconds. Arapan-S is available for free to the public. The binary files for Arapan-S are available through http://sourceforge.net/projects/dnascissor/files/.
has issue date	2012-05-16(xsd:dateTime)
bibo:doi	10.1186/1756-0500-5-243
bibo:pmid	22591859
has license	cc-by
sha1sum (hex)	7398c3a708a291677e55854601f643ba41d79916
schema:url	https://doi.org/10.1186/1756-0500-5-243
resource representing a document's title	Arapan-S: a fast and highly accurate whole-genome assembly software for viruses and small genomes
has PubMed Central identifier	PMC3441218
has PubMed identifier	22591859
schema:publication	BMC Res Notes
resource representing a document's body	covid:7398c3a708a291677e55854601f643ba41d79916#body_text
is schema:about of	named entity 'genomes' named entity 'assembly' named entity 'viruses' covid:arg/7398c3a708a291677e55854601f643ba41d79916 named entity 'general' named entity 'assemblers' named entity 'cases' named entity 'Genome assembly' named entity 'contigs' named entity 'assemblers' named entity 'genomes' named entity 'studied' named entity 'graph' named entity '64-bit' named entity 'assembler' named entity 'Hamiltonian path' named entity 'SNPs' named entity 'Influenza A Virus' named entity 'genome' named entity 'k-mer' named entity 'algorithm' named entity 'algorithm' named entity 'graph' named entity 'genomes' named entity 'algorithm' named entity 'algorithm' named entity 'EBI' named entity 'k-mers' named entity 'ncbi' named entity 'genome' named entity 'k-mer' named entity 'genome assembly' named entity 'connected component' named entity 'database' named entity 'genomes' named entity 'k-mer' named entity 'connected component' named entity 'k-mer' named entity 'depth-first search' named entity 'internal node' named entity 'genome' named entity 'Dijkstra' named entity 'genome' named entity 'Genome' named entity 'graph' named entity 'graph' named entity 'kmer' named entity 'length function' named entity 'genome' named entity 'graph' named entity 'CAP3' named entity 'genomes' named entity 'Euler' named entity 'graph' named entity 'k-mer' named entity 'de Bruijn' named entity 'sequencing errors' named entity 'algorithm' named entity 'graph' named entity 'QSRA' named entity 'algorithm' named entity 'breadth-first search' named entity 'assembler' named entity 'EBI' named entity 'nucleotide' named entity 'genomes' named entity 'algorithm' named entity 'k-mers' named entity 'NCBI' named entity 'subgraphs' named entity 'error correction' named entity 'NCBI BLAST' named entity 'de Bruijn' named entity 'graph' named entity 'contigs' named entity 'connected components' named entity 'Influenza A Virus' named entity 'genomes' named entity 'graph' named entity 'algorithm'

Faceted Search & Find service v1.13.91 as of Mar 24 2020

Alternative Linked Data Documents: Sponger | ODE Content Formats:

RDF

ODATA

Microdata

About

OpenLink Virtuoso version 07.20.3229 as of Jul 10 2020, on Linux (x86_64-pc-linux-gnu), Single-Server Edition (94 GB total memory)
Data on this page belongs to its respective rights holders.
Virtuoso Faceted Browser Copyright © 2009-2025 OpenLink Software