用于未校正的长纳米孔读数的快速从头布局的光谱算法
A spectral algorithm for fast de novo layout of uncorrected long nanopore reads
摘要：
动机：新的长读段测序仪有望通过产生数十个碱基长的读段来改变测序和基因组组装。然而，它们的高错误率显著地使组装复杂化，并且需要昂贵的校正步骤来使用标准组装引擎来布局读段。结果如下：我们提出了一个原始的和有效的光谱算法来布局未校正的纳米孔读取，并将其无缝集成到一个简单的重叠/布局/共识（OLC）组装方案。该方法显示将来自几种细菌基因组的Oxford Nanopore读数组装成高质量（与参考的同一性约99%）基因组大小的重叠群，同时从酿酒酵母参考菌株产生更多片段化的组装体。可用性和实施：http://github.com/antrec/spectrassembler联系人：antoine. inria.fr
英文摘要：
Motivation: New long read sequencers promise to transform sequencing and genome assembly by producing reads tens of kilobases long. However their high error rate significantly complicates assembly and requires expensive correction steps to layout the reads using standard assembly engines. Results: We present an original and efficient spectral algorithm to layout the uncorrected nanopore reads, and its seamless integration into a straightforward overlap/layout/consensus (OLC) assembly scheme. The method is shown to assemble Oxford Nanopore reads from several bacterial genomes into good quality (~99% identity to the reference) genome-sized contigs, while yielding more fragmented assemblies from a Sacharomyces cerevisiae reference strain. Availability and implementation: http://github.com/antrec/spectrassembler Contact: antoine.recanati@inria.fr
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