VSEARCH: a versatile open source tool for metagenomics
VSEARCH: a versatile open source tool for metagenomics
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DOI：
10.7717/peerj.2584
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发表时间：
2016-10-18
期刊：
影响因子：
2.7
通讯作者：
Mahe, Frederic
中科院分区：
文献类型：
--
作者：
Rognes, Torbjorn;Flouri, Tomas;Mahe, Frederic
背景Vectors是一个开源和免费的多线程64位工具，用于处理和准备宏基因组学，基因组学和群体基因组学核苷酸序列数据。它被设计为广泛使用的USESTIM工具（埃德加，2010年）的替代品，其源代码是不公开的，算法细节只是粗略描述，只有内存限制的32位版本可免费用于学术用途。当搜索核苷酸序列时，Vestro使用基于查询和目标序列共享的词的快速启发式算法，以便快速识别相似的序列，类似的策略可能在USEstro中使用。然后，VEGFR 2针对潜在的目标序列执行查询的最佳全局序列比对，使用完全动态编程而不是USERT 2使用的种子和扩展启发式。使用向量化和多线程并行计算成对比对。VESBLs包含了USESBLs第7版中提供的用于分析核苷酸序列的大多数命令，以及USESBLs第8版中提供的几个命令，包括搜索（精确或基于全局对齐），按相似性聚类（使用长度预分选、丰度预分选或用户定义的顺序）、嵌合体检测（基于参考或从头）、去复制（全长或前缀）、成对比对、反向互补、分选和二次取样。Vendix还包括用于FASTQ文件处理的命令，即，格式检测、过滤、读段质量统计和配对读段的合并。此外，Vendor通过几个新命令和改进扩展了功能，包括洗牌，重新复制，使用众所周知的DUST算法掩蔽低复杂度序列，在不同相似性定义中进行选择，以及FASTQ文件格式转换。在执行搜索、聚类、嵌合体检测和二次采样时，VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF-VEGF在执行聚类和嵌合体检测时，VEGF 10比USE 10慢，但在执行双端读段合并和去复制时，VEGF 10要快得多。Vibration可在https://github.com/torognes/vsearch上获得，使用BSD 2条款许可证或GNU通用公共许可证3.0版。事实证明，VEGFR 2是一种快速、准确和成熟的USEFR 2替代品。一个免费和开源的多功能序列分析工具现在可供宏基因组学社区使用。
Background. VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar, 2010) for which the source code is not publicly available, algorithm details are only rudimentarily described, and only a memory-confined 32-bit version is freely available for academic use.Methods. When searching nucleotide sequences, VSEARCH uses a fast heuristic based on words shared by the query and target sequences in order to quickly identify similar sequences, a similar strategy is probably used in USEARCH. VSEARCH then performs optimal global sequence alignment of the query against potential target sequences, using full dynamic programming instead of the seed-and-extend heuristic used by USEARCH. Pairwise alignments are computed in parallel using vectorisation and multiple threads.Results. VSEARCH includes most commands for analysing nucleotide sequences available in USEARCH version 7 and several of those available in USEARCH version 8, including searching (exact or based on global alignment), clustering by similarity (using length pre-sorting, abundance pre-sorting or a user-defined order), chimera detection (reference-based or de novo), dereplication (full length or prefix), pairwise alignment, reverse complementation, sorting, and subsampling. VSEARCH also includes commands for FASTQ file processing, i.e., format detection, filtering, read quality statistics, and merging of paired reads. Furthermore, VSEARCH extends functionality with several new commands and improvements, including shuffling, rereplication, masking of low-complexity sequences with the well-known DUST algorithm, a choice among different similarity definitions, and FASTQ file format conversion. VSEARCH is here shown to be more accurate than USEARCH when performing searching, clustering, chimera detection and subsampling, while on a par with USEARCH for paired-ends read merging. VSEARCH is slower than USEARCH when performing clustering and chimera detection, but significantly faster when performing paired-end reads merging and dereplication. VSEARCH is available at https://github.com/torognes/vsearch under either the BSD 2-clause license or the GNU General Public License version 3.0.Discussion. VSEARCH has been shown to be a fast, accurate and full-fledged alternative to USEARCH. A free and open-source versatile tool for sequence analysis is now available to the metagenomics community.