ASSIsT：一种用于自交和杂交物种的自动单核苷酸多态性评分工具。
ASSIsT: an automatic SNP scoring tool for in- and outbreeding species.
作者信息
Di Guardo Mario, Micheletti Diego, Bianco Luca, Koehorst-van Putten Herma J J, Longhi Sara, Costa Fabrizio, Aranzana Maria J, Velasco Riccardo, Arús Pere, Troggio Michela, van de Weg Eric W
机构信息
Wageningen UR Plant Breeding, 6700 AA Wageningen, The Netherlands, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy, Graduate School Experimental Plant Sciences, Wageningen University, 6700 AJ Wageningen, The Netherlands and.
Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy, Wageningen UR Plant Breeding, 6700 AA Wageningen, The Netherlands.
出版信息
Bioinformatics. 2015 Dec 1;31(23):3873-4. doi: 10.1093/bioinformatics/btv446. Epub 2015 Aug 6.
UNLABELLED
ASSIsT (Automatic SNP ScorIng Tool) is a user-friendly customized pipeline for efficient calling and filtering of SNPs from Illumina Infinium arrays, specifically devised for custom genotyping arrays. Illumina has developed an integrated software for SNP data visualization and inspection called GenomeStudio (GS). ASSIsT builds on GS-derived data and identifies those markers that follow a bi-allelic genetic model and show reliable genotype calls. Moreover, ASSIsT re-edits SNP calls with null alleles or additional SNPs in the probe annealing site. ASSIsT can be employed in the analysis of different population types such as full-sib families and mating schemes used in the plant kingdom (backcross, F1, F2), and unrelated individuals. The final result can be directly exported in the format required by the most common software for genetic mapping and marker-trait association analysis. ASSIsT is developed in Python and runs in Windows and Linux.
AVAILABILITY AND IMPLEMENTATION
The software, example data sets and tutorials are freely available at http://compbiotoolbox.fmach.it/assist/.
CONTACT
未标注
ASSIsT（自动单核苷酸多态性评分工具）是一个用户友好的定制流程，用于从Illumina Infinium阵列高效地调用和筛选单核苷酸多态性（SNP），特别为定制基因分型阵列设计。Illumina开发了一个名为GenomeStudio（GS）的用于SNP数据可视化和检查的集成软件。ASSIsT基于GS衍生的数据构建，并识别遵循双等位基因遗传模型且显示可靠基因型调用的那些标记。此外，ASSIsT会重新编辑在探针退火位点具有无效等位基因或额外SNP的SNP调用。ASSIsT可用于分析不同的群体类型，如植物界中使用的全同胞家系和交配方案（回交、F1、F2）以及无关个体。最终结果可以直接以最常见的用于遗传图谱绘制和标记 - 性状关联分析的软件所需的格式导出。ASSIsT是用Python开发的，可在Windows和Linux上运行。
可用性和实现方式
该软件、示例数据集和教程可在http://compbiotoolbox.fmach.it/assist/免费获取。
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