ELECTOR: evaluator for long reads correction methods.
ELECTOR: evaluator for long reads correction methods.
复制标题
DOI：
10.1093/nargab/lqz015
复制
发表时间：
2020-03
影响因子：
4.6
通讯作者：
Limasset A
中科院分区：
文献类型：
--
作者：
Marchet C;Morisse P;Lecompte L;Lefebvre A;Lecroq T;Peterlongo P;Limasset A
第三代测序数据的错误率上限> 5%，主要包含插入和缺失。因此，已经提出了越来越多的不同长读段校正方法。校正的质量对下游工艺产生巨大影响。因此，开发方法，允许评估误差校正工具与精确和可靠的统计是一个至关重要的需要。这些评估方法依赖于昂贵的比对来评估校正读数的质量。因此，关键功能必须允许不同工具的快速比较，并扩展到长读取的长度增加。我们的工具ELECTOR可评估长读取校正，并与各种错误校正工具直接兼容。由于它是基于多序列比对，我们引入了一种新的算法策略对齐分割，这使我们能够使用合理的资源扩展到大的实例。据我们所知，我们提供了一种独特的方法，可以在最新的超长读段（>100 k碱基）上产生可重现的校正基准。它也比其他数据集上的当前最新技术更快，并提供了更广泛的指标集来评估校正后的读取质量改善。ELECTOR可以在GitHub（https：//github.com/kamimrcht/ELECTOR）和Bioconda上找到。
The error rates of third-generation sequencing data have been capped >5%, mainly containing insertions and deletions. Thereby, an increasing number of diverse long reads correction methods have been proposed. The quality of the correction has huge impacts on downstream processes. Therefore, developing methods allowing to evaluate error correction tools with precise and reliable statistics is a crucial need. These evaluation methods rely on costly alignments to evaluate the quality of the corrected reads. Thus, key features must allow the fast comparison of different tools, and scale to the increasing length of the long reads. Our tool, ELECTOR, evaluates long reads correction and is directly compatible with a wide range of error correction tools. As it is based on multiple sequence alignment, we introduce a new algorithmic strategy for alignment segmentation, which enables us to scale to large instances using reasonable resources. To our knowledge, we provide the unique method that allows producing reproducible correction benchmarks on the latest ultra-long reads (>100 k bases). It is also faster than the current state-of-the-art on other datasets and provides a wider set of metrics to assess the read quality improvement after correction. ELECTOR is available on GitHub (https://github.com/kamimrcht/ELECTOR) and Bioconda.