MAPtools: command-line tools for mapping-by-sequencing and QTL-Seq analysis and visualization.

IF 4.7 2区生物学 Q1 BIOCHEMICAL RESEARCH METHODS

Plant Methods Pub Date : 2024-07-17 DOI:10.1186/s13007-024-01222-2

César Martínez-Guardiola, Ricardo Parreño, Héctor Candela

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引用次数: 0

Abstract

Background: Classical mutagenesis is a powerful tool that has allowed researchers to elucidate the molecular and genetic basis of a plethora of processes in many model species. The integration of these methods with modern massively parallel sequencing techniques, initially in model species but currently also in many crop species, is accelerating the identification of genes underlying a wide range of traits of agronomic interest.

Results: We have developed MAPtools, an open-source Python3 application designed specifically for the analysis of genomic data from bulked segregant analysis experiments, including mapping-by-sequencing (MBS) and quantitative trait locus sequencing (QTL-seq) experiments. We have extensively tested MAPtools using datasets published in recent literature.

Conclusions: MAPtools gives users the flexibility to customize their bioinformatics pipeline with various commands for calculating allele count-based statistics, generating plots to pinpoint candidate regions, and annotating the effects of SNP and indel mutations. While extensively tested with plants, the program is versatile and applicable to any species for which a mapping population can be generated and a sequenced genome is available.

Availability and implementation: MAPtools is available under GPL v3.0 license and documented as a Python3 package at https://github.com/hcandela/MAPtools .

查看原文本刊更多论文

MAPtools：用于测序制图和 QTL-Seq 分析及可视化的命令行工具。

背景：经典诱变是一种强大的工具，使研究人员能够在许多模式物种中阐明大量过程的分子和遗传基础。将这些方法与现代大规模并行测序技术相结合，最初是在模式物种中，目前也在许多作物物种中，正在加速鉴定农艺学感兴趣的各种性状的基础基因：我们开发了 MAPtools，这是一个开源 Python3 应用程序，专门用于分析批量分离分析实验的基因组数据，包括测序作图（MBS）和定量性状位点测序（QTL-seq）实验。我们使用最近发表的文献中的数据集对 MAPtools 进行了广泛测试：MAPtools 为用户提供了定制生物信息学管道的灵活性，用户可以使用各种命令计算基于等位基因计数的统计数据、生成图谱以精确定位候选区域，以及注释 SNP 和 indel 突变的影响。虽然该程序已在植物上进行了广泛测试，但其通用性很强，适用于任何可生成制图群体并可获得基因组测序的物种：MAPtools 在 GPL v3.0 许可下可用，并以 Python3 软件包的形式在 https://github.com/hcandela/MAPtools 上进行了记录。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Plant Methods 生物-植物科学

CiteScore

9.20

自引率

3.90%

发文量

121

审稿时长

2 months

期刊介绍： Plant Methods is an open access, peer-reviewed, online journal for the plant research community that encompasses all aspects of technological innovation in the plant sciences. There is no doubt that we have entered an exciting new era in plant biology. The completion of the Arabidopsis genome sequence, and the rapid progress being made in other plant genomics projects are providing unparalleled opportunities for progress in all areas of plant science. Nevertheless, enormous challenges lie ahead if we are to understand the function of every gene in the genome, and how the individual parts work together to make the whole organism. Achieving these goals will require an unprecedented collaborative effort, combining high-throughput, system-wide technologies with more focused approaches that integrate traditional disciplines such as cell biology, biochemistry and molecular genetics. Technological innovation is probably the most important catalyst for progress in any scientific discipline. Plant Methods’ goal is to stimulate the development and adoption of new and improved techniques and research tools and, where appropriate, to promote consistency of methodologies for better integration of data from different laboratories.