ASSIsT: an automatic SNP scoring tool for in- and outbreeding species

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 Geno...

Full description

Saved in:

Bibliographic Details
Published in:	Bioinformatics (Oxford, England) Vol. 31; no. 23; pp. 3873 - 3874
Main Authors:	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
Format:	Journal Article
Language:	English
Published:	England Oxford University Press 01-12-2015
Subjects:	Alleles Animals Applications Notes Genotyping Techniques - methods Humans Laboratorium voor Plantenveredeling Laboratory of Plant Breeding PBR Biodiversiteit en Genetische Variatie PBR Biodiversity and genetic variation PBR Ornamentals, tissue culture and gene transfer PBR Siergewassen, Tissue Culture Plant Breeding Polymorphism, Single Nucleotide Software WUR PB Biodiversiteit en Genetische Variatie WUR PB Siergewassen, Tissue Culture
Online Access:	Get full text
Tags:	Add Tag No Tags, Be the first to tag this record!

Description
Summary:	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. The software, example data sets and tutorials are freely available at http://compbiotoolbox.fmach.it/assist/. eric.vandeweg@wur.nl.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors. Associate Editor: Alfonso Valencia
ISSN:	1367-4803 1367-4811
DOI:	10.1093/bioinformatics/btv446