ModPhred：一个用于分析和存储纳米孔测序 DNA 和 RNA 修饰数据的集成工具包。
ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data.
机构信息
Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain.
International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland.
出版信息
Bioinformatics. 2021 Dec 22;38(1):257-260. doi: 10.1093/bioinformatics/btab539.
MOTIVATION
DNA and RNA modifications can now be identified using nanopore sequencing. However, we currently lack a flexible software to efficiently encode, store, analyze and visualize DNA and RNA modification data.
RESULTS
Here, we present ModPhred, a versatile toolkit that facilitates DNA and RNA modification analysis from nanopore sequencing reads in a user-friendly manner. ModPhred integrates probabilistic DNA and RNA modification information within the FASTQ and BAM file formats, can be used to encode multiple types of modifications simultaneously, and its output can be easily coupled to genomic track viewers, facilitating the visualization and analysis of DNA and RNA modification information in individual reads in a simple and computationally efficient manner.
AVAILABILITY AND IMPLEMENTATION
ModPhred is available at https://github.com/novoalab/modPhred, is implemented in Python3, and is released under an MIT license. Docker images with all dependencies preinstalled are also provided.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
动机
现在可以使用纳米孔测序来鉴定 DNA 和 RNA 修饰。然而，我们目前缺乏一种灵活的软件，无法有效地对 DNA 和 RNA 修饰数据进行编码、存储、分析和可视化。
结果
在这里，我们展示了 ModPhred，这是一个通用的工具包，以用户友好的方式促进来自纳米孔测序读取的 DNA 和 RNA 修饰分析。ModPhred 在 FASTQ 和 BAM 文件格式中集成了概率 DNA 和 RNA 修饰信息，可以同时用于编码多种类型的修饰，并且其输出可以轻松与基因组轨迹查看器耦合，以简单和高效的计算方式促进单个读取中 DNA 和 RNA 修饰信息的可视化和分析。
可用性和实现
ModPhred 可在 https://github.com/novoalab/modPhred 获得，它是用 Python3 实现的，并根据 MIT 许可证发布。还提供了所有依赖项预先安装的 Docker 映像。
补充信息
补充数据可在 Bioinformatics 在线获得。
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