ArticleBMC bioinformatics2014
CAR: contig assembly of prokaryotic draft genomes using rearrangements.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- A thermophilic chemolithoautotrophic bacterial consortium suggests a mutual relationship between bacteria in extreme oligotrophic environments.Communications biology · 2023Article
- An IntranuclearMicroorganisms · 2020Article
- Comparative genomic analysis identifies X-factor (haemin)-independentMicrobial genomics · 2020Article
- Campylobacter jejuni isolated from poultry meat in Brazil: in silico analysis and genomic features of two strains with different phenotypes of antimicrobial susceptibility.Molecular biology reports · 2020Article
- Modern technologies and algorithms for scaffolding assembled genomes.PLoS computational biology · 2019Review
- Strain- and Species-Level Variation in the Microbiome of Diabetic Wounds Is Associated with Clinical Outcomes and Therapeutic Efficacy.Cell host & microbe · 2019Article
- Genome sequence of Xanthomonas fuscans subsp. fuscans strain Xff49: a new isolate obtained from common beans in Southern Brazil.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2019Article
- Multi-CSAR: a multiple reference-based contig scaffolder using algebraic rearrangements.BMC systems biology · 2018Article
- CSAR-web: a web server of contig scaffolding using algebraic rearrangements.Nucleic acids research · 2018Article
- Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes.BMC genomics · 2018Article
- Whole-genome sequencing of Leptospira interrogans from southern Brazil: genetic features of a highly virulent strain.Memorias do Instituto Oswaldo Cruz · 2018Article
- Complete genome sequence of nativeData in brief · 2018Article
- Complete Genome Sequence ofGenome announcements · 2018Article
- Genome Analysis of Haplotype D ofFrontiers in microbiology · 2018Article
- Multi-CAR: a tool of contig scaffolding using multiple references.BMC bioinformatics · 2016Article
- Comparative Genomic Analysis of Sulfurospirillum cavolei MES Reconstructed from the Metagenome of an Electrosynthetic Microbiome.PloS one · 2016Article
- Draft Genome Sequence of Clavibacter michiganensis subsp. nebraskensis Strain DOAB 397, Isolated from an Infected Field Corn Plant in Manitoba, Canada.Genome announcements · 2015Article
- Genomic and Functional Characterization of qnr-Encoding Plasmids from Municipal Wastewater Biosolid Klebsiella pneumoniae Isolates.Frontiers in microbiology · 2015Article
- Approaches for in silico finishing of microbial genome sequences.Genetics and molecular biologyArticle
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNext generation sequencing technology has allowed efficient production of draft genomes for many organisms of interest. However, most draft genomes are just collections of independent contigs, whose relative positions and orientations along the genome being sequenced are unknown. Although several tools have been developed to order and orient the contigs of draft genomes, more accurate tools are still needed.
resultsIn this study, we present a novel reference-based contig assembly (or scaffolding) tool, named as CAR, that can efficiently and more accurately order and orient the contigs of a prokaryotic draft genome based on a reference genome of a related organism. Given a set of contigs in multi-FASTA format and a reference genome in FASTA format, CAR can output a list of scaffolds, each of which is a set of ordered and oriented contigs. For validation, we have tested CAR on a real dataset composed of several prokaryotic genomes and also compared its performance with several other reference-based contig assembly tools. Consequently, our experimental results have shown that CAR indeed performs better than all these other reference-based contig assembly tools in terms of sensitivity, precision and genome coverage.
conclusionsCAR serves as an efficient tool that can more accurately order and orient the contigs of a prokaryotic draft genome based on a reference genome. The web server of CAR is freely available at http://genome.cs.nthu.edu.tw/CAR/ and its stand-alone program can also be downloaded from the same website.
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