Motivation: DNA sequence reads from Sanger and pyrosequencing platforms differ in cost, accuracy, typical coverage, average read length and the variety of available paired-end protocols. Both read types can complement one another in a 'hybrid' approach to whole-genome shotgun sequencing projects, but assembly software must be modified to accommodate their different characteristics. This is true even of pyrosequencing mated and unmated read combinations. Without special modifications, assemblers tuned for homogeneous sequence data may perform poorly on hybrid data.
Results: Celera Assembler was modified for combinations of ABI 3730 and 454 FLX reads. The revised pipeline called CABOG (Celera Assembler with the Best Overlap Graph) is robust to homopolymer run length uncertainty, high read coverage and heterogeneous read lengths. In tests on four genomes, it generated the longest contigs among all assemblers tested. It exploited the mate constraints provided by paired-end reads from either platform to build larger contigs and scaffolds, which were validated by comparison to a finished reference sequence. A low rate of contig mis-assembly was detected in some CABOG assemblies, but this was reduced in the presence of sufficient mate pair data.
Availability: The software is freely available as open-source from http://wgs-assembler.sf.net under the GNU Public License.
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http://dx.doi.org/10.1093/bioinformatics/btn548 | DOI Listing |
J Glob Antimicrob Resist
December 2021
Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China. Electronic address:
Objectives: Aeromonas veronii can cause infections in humans and a wide variety of aquatic and terrestrial animals as well as causing serious economic losses in aquaculture worldwide. Aeromonas veronii strain JC529 was isolated from an infected common carp in a fish pond in Jilin Province. In this study, we identified the multidrug resistance genes and traced the source of the strain in order to lay the foundation for research on the resistance mechanisms of other Aeromonas isolates.
View Article and Find Full Text PDFJ Glob Antimicrob Resist
March 2020
Department of Pathogenic Biology, School of Basic Medicine, Southwest Medical University, No. 319 Zhongshan Road, Luzhou 646000, Sichuan, China. Electronic address:
Objectives: The aim of this study was to characterise a high biofilm-forming capacity, hypermucoviscous, bla and bla co-producing Klebsiella pneumoniae strain (KSH203).
Methods: Antimicrobial susceptibility, biofilm formation and hypermucoviscous phenotype were determined by the disk diffusion method, crystal violet staining and positive string test, respectively. Whole-genome sequencing was performed using a PacBio RS II Sequencer.
J Glob Antimicrob Resist
March 2019
Department of Physiology, School of Basic Medicine, Southwest Medical University, No. 1 Xianglin Road, Luzhou, Sichuan, China.
Objectives: Acinetobacter spp. isolates carrying the bla gene are frequently reported. However, most reported bla genes are carried by clinical strains.
View Article and Find Full Text PDFGenome Res
May 2017
Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
G3 (Bethesda)
March 2017
School of Biological Sciences, The University of Queensland, St Lucia, Queensland 4072, Australia
Long-read sequencing technology promises to greatly enhance assembly of genomes for nonmodel species. Although the error rates of long reads have been a stumbling block, sequencing at high coverage permits the self-correction of many errors. Here, we sequence and assemble the genome of , a species from the subgroup that has been well-studied for latitudinal clines, sexual selection, and gene expression, but which lacks a reference genome.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!