论文标题
语法压缩机，用于收集读取的读取，并应用于BWT的构建
A grammar compressor for collections of reads with applications to the construction of the BWT
论文作者
论文摘要
我们描述了用于DNA测序读取的语法，我们可以直接计算BWT。我们的动机是进行简洁的空间基因组分析，这些分析需要基于重复的自我索引支持的复杂弦查询。我们的方法是将一组读取作为语法存储，但是在需要时，请计算其BWT以使用自我索引进行分析。我们在实际数据中进行的实验表明，我们使用压缩机实现的空间缩短具有基于LZ的方法，并且比基于熵的方法更好。与其他流行的语法相比，在这种数据中，我们平均达到了额外压缩的12％，并且需要更少的工作空间和时间。
We describe a grammar for DNA sequencing reads from which we can compute the BWT directly. Our motivation is to perform in succinct space genomic analyses that require complex string queries not yet supported by repetition-based self-indexes. Our approach is to store the set of reads as a grammar, but when required, compute its BWT to carry out the analysis by using self-indexes. Our experiments in real data showed that the space reduction we achieve with our compressor is competitive with LZ-based methods and better than entropy-based approaches. Compared to other popular grammars, in this kind of data, we achieve, on average, 12\% of extra compression and require less working space and time.
