caprg sequence assembling pipeline for next generation sequencing of non-model organismscaprg序列组装管道non-model下一代测序的生物.pdfVIP

CAPRG: Sequence Assembling Pipeline for Next Generation Sequencing of Non-Model Organisms 1,2 2 3 4 5 5 Arun Rawat *, Mohamed O. Elasri , Kurt A. Gust , Glover George , Don Pham , Leona D. Scanlan , Chris 5 3 Vulpe , Edward J. Perkins * 1 Center for Pathogen Information, Translational Genomics Research Institute North, Flagstaff, Arizona, United States of America, 2 Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, Mississippi, United States of America, 3 Environmental Laboratory, EP-P, U.S. Army Engineer Research and Development Center, Vicksburg, Mississippi, United States of America, 4 School of Computing Science, University of Southern Mississippi, Hattiesburg, Mississippi, United States of America, 5 Department of Nutritional Science and Toxicology, University of California, Berkeley, California, United States of America Abstract Our goal is to introduce and describe the utility of a new pipeline ‘‘Contigs Assembly Pipeline using Reference Genome’’ (CAPRG), which has been developed to assemble ‘‘long sequence reads’’ for non-model organisms by leveraging a reference genome of a closely related phylogenetic relative. To facilitate this effort, we utilized two avian transcriptomic datasets generated using ROCHE/454 technology as test cases for CAPRG assembly. We compared the results of CAPRG assembly using a reference genome with the results of existing methods that utilize de novo strategies such as VELVET, PAVE, and MIRA by employing parameter space comparisons (intra-assembling comparison). CAPRG performed as well or better than the existing assembly methods based on various benchmarks for ‘‘gene-hunting.’’ Furthe