NGseqBasic - a single-command UNIX tool for ATAC-seq, DNaseI-seq, Cut-and-Run, and ChIP-seq data mapping, high-resolution visualisation, and quality control
NGseqBasic - a single-command UNIX tool for ATAC-seq, DNaseI-seq, Cut-and-Run, and ChIP-seq data mapping, high-resolution visualisation, and quality control
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NGseqBasic - 用于 ATAC-seq、DNaseI-seq、Cut-and-Run 和 ChIP-seq 数据映射、高分辨率可视化和质量控制的单命令 UNIX 工具
DOI：
10.1101/393413
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发表时间：
2018
期刊：
影响因子：
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通讯作者：
J. Hughes
中科院分区：
文献类型：
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作者：
Jelena M. Telenius;J. Hughes
随着下一代测序（NGS）成本的下降，我们正在观察到学术研究、医疗保健和药物发现领域的“大数据”量的快速增长。目前从这些“大数据”集中提取价值的瓶颈是数据处理和分析。考虑到这一点，仍然缺乏可靠、自动化和易于使用的工具，使实验人员能够评估测序库的质量并第一手探索数据，而不需要在分析的早期阶段投入大量的计算核心分析时间。NGseqBasic是一个易于使用的单命令分析工具，用于染色质可及性（ATAC, DNaseI）和ChIP测序数据，为低细胞数测序和Cut-and-Run等新技术提供支持。它采用fastq， fastq.gz或bam文件，进行所有质量控制，修剪和映射步骤，以及质量控制和数据处理统计，并将所有这些结合到一个点击可加载的UCSC数据中心，与积分统计html页面提供详细的报告从分析工具和质量控制指标。该工具易于设置，无需安装。各种各样的参数提供微调分析，可选的设置，以产生dna足迹或高分辨率ChIP-seq轨道。提供了一个测试脚本来帮助设置，以及一个测试数据集和可下载的示例用户用例。NGseqBasic已被用于高影响力出版物中下一代测序（NGS）数据的常规分析1,2。代码是积极开发的，并伴随着Git版本控制和Github代码存储库。在这里，我们使用来自GSM689849的DNaseI-seq数据和来自GSM2579421的CTCF- chip -seq数据以及Cut-and-Run CTCF数据集GSM2433142演示NGseqBasic的分析和特征，并提供由工具生成的一键式可加载UCSC数据中心，允许随时探索由工具生成的运行结果和质量控制文件。下载、设置和帮助说明可在NGseqBasic网站http://userweb.molbiol.ox.ac.uk/public/telenius/NGseqBasicManual/external/上获得。Bioconda用户可以将该工具加载为库“NGseqBasic”。Git版本控制的源代码可从https://github.com/Hughes-Genome-Group/NGseqBasic/releases获得。接触jelena.telenius@imm.ox.ac.uk
With decreasing cost of next-generation sequencing (NGS), we are observing a rapid rise in the volume of ‘big data’ in academic research, healthcare and drug discovery sectors. The present bottleneck for extracting value from these ‘big data’ sets is data processing and analysis. Considering this, there is still a lack of reliable, automated and easy to use tools that will allow experimentalists to assess the quality of the sequenced libraries and explore the data first hand, without the need of investing a lot of time of computational core analysts in the early stages of analysis. NGseqBasic is an easy-to-use single-command analysis tool for chromatin accessibility (ATAC, DNaseI) and ChIP sequencing data, providing support to also new techniques such as low cell number sequencing and Cut-and-Run. It takes in fastq, fastq.gz or bam files, conducts all quality control, trimming and mapping steps, along with quality control and data processing statistics, and combines all this to a single-click loadable UCSC data hub, with integral statistics html page providing detailed reports from the analysis tools and quality control metrics. The tool is easy to set up, and no installation is needed. A wide variety of parameters are provided to fine-tune the analysis, with optional setting to generate DNase footprint or high resolution ChIP-seq tracks. A tester script is provided to help in the setup, along with a test data set and downloadable example user cases. NGseqBasic has been used in the routine analysis of next generation sequencing (NGS) data in high-impact publications 1,2. The code is actively developed, and accompanied with Git version control and Github code repository. Here we demonstrate NGseqBasic analysis and features using DNaseI-seq data from GSM689849, and CTCF-ChIP-seq data from GSM2579421, as well as a Cut-and-Run CTCF data set GSM2433142, and provide the one-click loadable UCSC data hubs generated by the tool, allowing for the ready exploration of the run results and quality control files generated by the tool. Availability Download, setup and help instructions are available on the NGseqBasic web site http://userweb.molbiol.ox.ac.uk/public/telenius/NGseqBasicManual/external/ Bioconda users can load the tool as library “ngseqbasic”. The source code with Git version control is available in https://github.com/Hughes-Genome-Group/NGseqBasic/releases. Contact jelena.telenius@imm.ox.ac.uk