RazerS 3: Faster, fully sensitive read mapping
RazerS 3: Faster, fully sensitive read mapping
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DOI：
10.1093/bioinformatics/bts505
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发表时间：
2012-10-15
期刊：
影响因子：
5.8
通讯作者：
Reinert, Knut
中科院分区：
文献类型：
--
作者：
Weese, David;Holtgrewe, Manuel;Reinert, Knut
动机：在过去的几年里，下一代测序已经成为生物医学科学中许多应用的关键技术。吞吐量继续增加，新的协议提供比当前可用的更长的读取时间。在几乎所有的应用中，读取映射是第一步。因此，它是至关重要的算法和实现，执行速度快，灵敏度高，并能够处理长的读取和大量的绝对数量的插入和deletions.Results：RazerS是一个读取映射程序与可调的灵敏度的基础上计数q-gram。在这项工作中，我们提出了继任者RazerS 3，它现在支持共享内存并行，一个额外的基于种子的过滤器，具有可调节的灵敏度，一个更快的，带状版本的迈尔斯的位向量算法的验证，内存节省措施和支持SAM输出格式。这大大提高了映射读取的性能，特别是具有许多错误的长读取。我们将RazerS 3与其他流行的读取映射器进行了广泛的比较，并表明其结果在灵敏度方面往往上级它们，同时表现出实用且通常具有竞争力的运行时间。此外，RazerS 3没有预先计算的索引。
Motivation: During the past years, next-generation sequencing has become a key technology for many applications in the biomedical sciences. Throughput continues to increase and new protocols provide longer reads than currently available. In almost all applications, read mapping is a first step. Hence, it is crucial to have algorithms and implementations that perform fast, with high sensitivity, and are able to deal with long reads and a large absolute number of insertions and deletions.Results: RazerS is a read mapping program with adjustable sensitivity based on counting q-grams. In this work, we propose the successor RazerS 3, which now supports shared-memory parallelism, an additional seed-based filter with adjustable sensitivity, a much faster, banded version of the Myers' bit-vector algorithm for verification, memory-saving measures and support for the SAM output format. This leads to a much improved performance for mapping reads, in particular, long reads with many errors. We extensively compare RazerS 3 with other popular read mappers and show that its results are often superior to them in terms of sensitivity while exhibiting practical and often competitive run times. In addition, RazerS 3 works without a pre-computed index.