FSG：用于读取数据从头组装的快速字符串图构造
FSG: Fast String Graph Construction for De Novo Assembly of Reads Data
摘要：
下一代读取集合的字符串图是一种无损数据表示，对于基于重复布局共识范式的从头组装器来说是基本的。在本文中，我们探索了一种新的方法来计算弦图，基于FM指数和Burrows-Wheeler变换。我们描述了一个简单的算法，只使用FM索引表示的读取集合来构建字符串图，而不访问输入读取。我们的算法已被集成到SGA汇编程序作为一个独立的模块来构建字符串图。新的集成汇编程序已在标准基准上进行了评估，表明FSG比SGA快得多，同时保持适度使用主存，并在多线程上运行FSG时显示出实际优势。
英文摘要：
The string graph for a collection of next-generation reads is a lossless data representation that is fundamental for de novo assemblers based on the overlap-layout-consensus paradigm. In this paper, we explore a novel approach to compute the string graph, based on the FM-index and Burrows-Wheeler Transform. We describe a simple algorithm that uses only the FM-index representation of the collection of reads to construct the string graph, without accessing the input reads. Our algorithm has been integrated into the SGA assembler as a standalone module to construct the string graph. The new integrated assembler has been assessed on a standard benchmark, showing that FSG is significantly faster than SGA while maintaining a moderate use of main memory, and showing practical advantages in running FSG on multiple threads.
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