an integrated pipeline for de novo assembly of microbial genomes一个集成的管道为新创微生物基因组的组装.pdfVIP

An Integrated Pipeline for de Novo Assembly of Microbial Genomes 1 1,2,3 1,4 1 Andrew Tritt , Jonathan A. Eisen , Marc T. Facciotti , Aaron E. Darling * 1 Genome Center, University of California Davis, Davis, California, United States of America, 2 Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America, 3 Department of Medical Microbiology and Immunology, University of California Davis, Davis, California, United States of America, 4 Department of Biomedical Engineering, University of California Davis, Davis, California, United States of America Abstract Remarkable advances in DNA sequencing technology have created a need for de novo genome assembly methods tailored to work with the new sequencing data types. Many such methods have been published in recent years, but assembling raw sequence data to obtain a draft genome has remained a complex, multi-step process, involving several stages of sequence data cleaning, error correction, assembly, and quality control. Successful application of these steps usually requires intimate knowledge of a diverse set of algorithms and software. We present an assembly pipeline called A5 (Andrew And Aaron’s Awesome Assembly pipeline) that simplifies the entire genome assembly process by automating these stages, by integrating several previously published algorithms with new algorithms for quality control and automated assembly parameter selection. We demonstrate that A5 can produce assemblies of quality comparable to a leading assembly algorithm, SOAPdenovo, without any prior knowledge of the particular genome being assembled and without the extensive parameter tuning required by the o