quake quality-aware detection and correction of sequencing errors地震quality-aware测序错误检测和校正.pdfVIP

Kelley et al. Genome Biology 2010, 11:R116 /2010/11/11/R116 SOFTWARE Open Access Quake: quality-aware detection and correction of sequencing errors 1* 2 1 David R Kelley , Michael C Schatz , Steven L Salzberg Abstract We introduce Quake, a program to detect and correct errors in DNA sequencing reads. Using a maximum likeli- hood approach incorporating quality values and nucleotide specific miscall rates, Quake achieves the highest accu- racy on realistically simulated reads. We further demonstrate substantial improvements in de novo assembly and SNP detection after using Quake. Quake can be used for any size project, including more than one billion human reads, and is freely available as open source software from /software/quake. Rationale may create ambiguous paths or improperly connect Massively parallel DNA sequencing has become a promi- remote regions of the genome [7]. In genome re-sequen- nent tool in biological research [1,2]. The high-through- cing projects, reads are aligned to a reference genome, put and low cost of second-generation sequencing usually allowing for a fixed number of mismatches due technologies has allowed researchers to address an ever- to either SNPs or sequencing errors [8]. In most cases, larger set of biological and biomedical problems. For the reference genome and the genome being newly example, the 1000 Genomes Project is using sequencing sequenced will differ, sometimes substantially. Variable to discover all common variations in the human genome regions are more difficult to align because mismatches [3]. The Genome 10K Project plans