FROGS：使用 Galaxy 解决方案快速找到 OTUs。

FROGS: Find, Rapidly, OTUs with Galaxy Solution.

机构信息

Bioinformatics platform Toulouse Midi-Pyrenees, MIAT, INRA Auzeville CS 52627 31326 Castanet Tolosan cedex, France.

INRA, UMR 1136, Université de Lorraine, INRA-Nancy, 54280, Champenoux, France.

出版信息

Bioinformatics. 2018 Apr 15;34(8):1287-1294. doi: 10.1093/bioinformatics/btx791.

DOI:10.1093/bioinformatics/btx791

PMID:29228191

Abstract

MOTIVATION

Metagenomics leads to major advances in microbial ecology and biologists need user friendly tools to analyze their data on their own.

RESULTS

This Galaxy-supported pipeline, called FROGS, is designed to analyze large sets of amplicon sequences and produce abundance tables of Operational Taxonomic Units (OTUs) and their taxonomic affiliation. The clustering uses Swarm. The chimera removal uses VSEARCH, combined with original cross-sample validation. The taxonomic affiliation returns an innovative multi-affiliation output to highlight databases conflicts and uncertainties. Statistical results and numerous graphical illustrations are produced along the way to monitor the pipeline. FROGS was tested for the detection and quantification of OTUs on real and in silico datasets and proved to be rapid, robust and highly sensitive. It compares favorably with the widespread mothur, UPARSE and QIIME.

AVAILABILITY AND IMPLEMENTATION

Source code and instructions for installation: https://github.com/geraldinepascal/FROGS.git. A companion website: http://frogs.toulouse.inra.fr.

CONTACT

geraldine.pascal@inra.fr.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

动机

宏基因组学推动了微生物生态学的重大进展，生物学家需要用户友好的工具来自行分析数据。

结果

这个名为 FROGS 的 Galaxy 支持的管道旨在分析大量扩增子序列，并生成操作分类单元（OTUs）及其分类归属的丰度表。聚类使用 Swarm。嵌合体去除使用 VSEARCH，结合原始交叉样本验证。分类归属返回了一种创新的多归属输出，以突出数据库冲突和不确定性。在整个过程中生成统计结果和大量图形说明，以监测管道。FROGS 已针对真实和虚拟数据集上的 OTUs 检测和定量进行了测试，结果证明其快速、稳健且高度敏感。它与广泛使用的 mothur、UPARSE 和 QIIME 相比具有优势。