The construction of a suffix array for a collection of strings is a fundamental task in Bioinformatics and in many other applications that process strings. Related data structures, as the Longest Common Prefix array, the Burrows–Wheeler transform, and the document array, are often needed to accompany the suffix array to efficiently solve a wide variety of problems. While several algorithms have been proposed to construct the suffix array for a single string, less emphasis has been put on algorithms to construct suffix arrays for string collections. In this paper we introduce gsufsort, an open source software for constructing the suffix array and related data indexing structures for a string collection with N symbols in O(N) time. Our tool is written in ANSI/C and is based on the algorithm gSACA-K (Louza et al. in Theor Comput Sci 678:22–39, 2017), the fastest algorithm to construct suffix arrays for string collections. The tool supports large fasta, fastq and text files with multiple strings as input. Experiments have shown very good performance on different types of strings. gsufsort is a fast, portable, and lightweight tool for constructing the suffix array and additional data structures for string collections.

中文翻译：

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gsufsort：为字符串集合构建后缀数组、LCP数组和BWT

为字符串集合构建后缀数组是生物信息学和许多其他处理字符串的应用程序中的一项基本任务。相关的数据结构，如最长公共前缀数组、Burrows-Wheeler 变换和文档数组，通常需要伴随后缀数组来有效解决各种各样的问题。虽然已经提出了几种算法来构造单个字符串的后缀数组，但较少强调为字符串集合构造后缀数组的算法。在本文中，我们介绍了 gsufsort，这是一个开源软件，用于在 O(N) 时间内为具有 N 个符号的字符串集合构建后缀数组和相关的数据索引结构。我们的工具是用 ANSI/C 编写的，基于算法 gSACA-K（Louza 等人在 Theor Comput Sci 678:22–39, 2017），为字符串集合构建后缀数组的最快算法。该工具支持带有多个字符串作为输入的大型 fasta、fastq 和文本文件。实验表明，在不同类型的字符串上性能非常好。gsufsort 是一种快速、可移植且轻量级的工具，用于为字符串集合构建后缀数组和其他数据结构。