Background: With the rapid development of the next generation sequencing (NGS) technology, large quantities of\r\ngenome sequencing data have been generated. Because of repetitive regions of genomes and some other factors,\r\nassembly of very short reads is still a challenging issue.\r\nResults: A novel strategy for improving genome assembly from very short reads is proposed. It can increase\r\naccuracies of assemblies by integrating de novo contigs, and produce comparative contigs by allowing multiple\r\nreferences without limiting to genomes of closely related strains. Comparative contigs are used to scaffold de novo\r\ncontigs. Using simulated and real datasets, it is shown that our strategy can effectively improve qualities of\r\nassemblies of isolated microbial genomes and metagenomes.\r\nConclusions: With more and more reference genomes available, our strategy will be useful to improve qualities of\r\ngenome assemblies from very short reads. Some scripts are provided to make our strategy applicable at http://\r\ncode.google.com/p/cd-hybrid/.
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