NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles.
NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles.
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DOI：
10.1093/bioinformatics/btv540
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发表时间：
2016-01-01
期刊：
影响因子：
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通讯作者：
Davey RP
中科院分区：
文献类型：
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作者：
Leggett RM;Heavens D;Caccamo M;Clark MD;Davey RP
动机：Oxford Nanopore MinION 测序仪目前正在通过 MinION Access Program (MAP) 进行预发布测试，有望通过廉价、紧凑的 USB 设备进行长时间实时读取。已经发布了从 MinION 碱基检出输出中提取 FASTA/Q 并提供基本产量统计数据的工具。然而，目前还没有单一工具可以提供基于对齐的全面质量控制和错误曲线分析——考虑到平台发展的速度，这一点极其重要。结果：NanoOK 生成详细的表格和图形输出以及深入的多页 PDF 报告，包括错误概况、质量和良率数据。 NanoOK 是多参考的，可以对宏基因组或多路样本进行详细分析。支持四种流行的纳米孔对准器，并且可以轻松扩展以包括其他对准器。可用性和实施：NanoOK 是一款开源软件，用 Java 实施，并支持 R 脚本。它已经在 Linux 和 Mac OS X 上进行了测试，可以从 https://github.com/TGAC/NanoOK 下载。包含本文中使用的所有依赖项和 DH10B 读取集的 VirtualBox VM 可从 http://opendata.tgac.ac.uk/nanook/ 获取。 Docker 镜像也可从 Docker Hub 获取 - 请参阅程序文档 https://documentation.tgac.ac.uk/display/NANOOK。联系方式：richard.leggett@tgac.ac.uk 补充信息：补充数据可在生物信息学在线获取。
Motivation: The Oxford Nanopore MinION sequencer, currently in pre-release testing through the MinION Access Programme (MAP), promises long reads in real-time from an inexpensive, compact, USB device. Tools have been released to extract FASTA/Q from the MinION base calling output and to provide basic yield statistics. However, no single tool yet exists to provide comprehensive alignment-based quality control and error profile analysis—something that is extremely important given the speed with which the platform is evolving. Results: NanoOK generates detailed tabular and graphical output plus an in-depth multi-page PDF report including error profile, quality and yield data. NanoOK is multi-reference, enabling detailed analysis of metagenomic or multiplexed samples. Four popular Nanopore aligners are supported and it is easily extensible to include others. Availability and implementation: NanoOK is an open-source software, implemented in Java with supporting R scripts. It has been tested on Linux and Mac OS X and can be downloaded from https://github.com/TGAC/NanoOK. A VirtualBox VM containing all dependencies and the DH10B read set used in this article is available from http://opendata.tgac.ac.uk/nanook/. A Docker image is also available from Docker Hub—see program documentation https://documentation.tgac.ac.uk/display/NANOOK. Contact: richard.leggett@tgac.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.