ArticleBMC bioinformatics2011
A new strategy for better genome assembly from very short reads.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Interpreting antimicrobial resistance from bacterial whole-genome sequencing: prediction tools, database fragmentation, analytical trade-offs, and harmonized reporting.Frontiers in microbiology · 2026Review
- Genome-Wide Development and Characterization of Microsatellite Markers in the Great Web-Spinning SawflyEcology and evolution · 2024Article
- The endophytome (plant-associated microbiome): methodological approaches, biological aspects, and biotech applications.World journal of microbiology & biotechnology · 2021Review
- Chromatin structure analysis enables detection of DNA insertions into the mammalian nuclear genome.Biochemistry and biophysics reports · 2015Article
- Metagenomic identification of novel enteric viruses in urban wild rats and genome characterization of a group A rotavirus.The Journal of general virology · 2014Article
- A scalable and accurate targeted gene assembly tool (SAT-Assembler) for next-generation sequencing data.PLoS computational biology · 2014Article
- Microevolution of Renibacterium salmoninarum: evidence for intercontinental dissemination associated with fish movements.The ISME journal · 2014Article
- A base composition analysis of natural patterns for the preprocessing of metagenome sequences.BMC bioinformatics · 2013Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWith the rapid development of the next generation sequencing (NGS) technology, large quantities of genome sequencing data have been generated. Because of repetitive regions of genomes and some other factors, assembly of very short reads is still a challenging issue.
resultsA novel strategy for improving genome assembly from very short reads is proposed. It can increase accuracies of assemblies by integrating de novo contigs, and produce comparative contigs by allowing multiple references without limiting to genomes of closely related strains. Comparative contigs are used to scaffold de novo contigs. Using simulated and real datasets, it is shown that our strategy can effectively improve qualities of assemblies of isolated microbial genomes and metagenomes.
conclusionsWith more and more reference genomes available, our strategy will be useful to improve qualities of genome assemblies from very short reads. Some scripts are provided to make our strategy applicable at http://code.google.com/p/cd-hybrid/.
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