2008년 6월 18일 수요일

454/Sanger hybrid assembly에 대한 간단한 논문

공개된 소프트웨어 도구를 이용하여 454/Sanger data의 혼합 유전체 서열단편 합체를 하는 일반적인 전략을 다루는 간단한 논문을 국내 학술지에 투고중이다. 이 과정에 대하여 궁금해 하는 사람들이 많아서, 복잡한 내용은 아니라 하더라도 어떤 형태로든 발표를 하고 싶었었다. 좋은 결과가 나오기를!

한국유전체학회의 국내 저널에 실렸다. PDF 파일을 임으로 웹에 게시할 수는 없으므로 초록을 포함한 서지 정보만 수록하도록 한다.

Haeyoung Jeong and Jihyun F. Kim
Genomics & Informatics 6(2) 87-90, 2008
An optimized strategy for genome assembly of Sanger/pyrosequencing hybrid data using available software.

During the last four years, the pyrosequencing-based454 platform has rapidly displaced the traditional Sangersequencing method due to its high throughput and costeffectiveness. Meanwhile, the Sanger sequencing methodologystill provides the longest reads, and paired-endsequencing that is based on that chemistry offers anopportunity to ensure accurate assembly results. In thisreport, we describe an optimized approach for hybrid denovo genome assembly using pyrosequencing data andvarying amounts of Sanger-type reads. 454 platformderivedcontigs can be used as single non-breakablevirtual reads or converted to simpler contigs that consistof editable, overlapping pseudoreads. These modifiedcontigs maintain their integrity at the first jumpstartingassembly stage and are edited by fragmenting andrejoining. Pre-existing assembly software then can beapplied for mixed assembly with 454-derived data andSanger reads. An effective method for identifying genomicdifferences between reference and sample sequencesin whole-genome resequencing procedures alsois suggested.