ASSIsT specifications


Unique identifier OMICS_09713
Alternative name Automatic SNP ScorIng Tool
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data ASSIsT requires three input files: a pedigree file in which the parents of each sample are reported and two standard report files from GS (Final Report and DNA Report). The two GS reports are standard output of commercial service companies.
Output data Results can be exported to different formats and therefore can be fed straight to marker-trait association analysis software like FlexQTL, HapMap, GAPIT, JoinMap, PLINK, Structure and Tassel.
Biological technology Illumina
Operating system Unix/Linux, Windows
Programming languages Python
License GNU General Public License version 2.0
Computer skills Medium
Stability Stable
Maintained Yes


No version available


  • person_outline Eric W. van de Weg

Publication for Automatic SNP ScorIng Tool

ASSIsT citation


Biotechnology and apple breeding in Japan

Breed Sci
PMCID: 4780799
PMID: 27069388
DOI: 10.1270/jsbbs.66.18

[…] n genomics and breeding (, ). The project ended on August 31st, 2015 with the generation of new tools for phenotyping, genotyping and transcriptomics such as ASSIsT, an automatic SNP scoring tool for the selection of high-quality reliable markers (). […]

ASSIsT institution(s)
Wageningen UR Plant Breeding, AA Wageningen, Netherlands; Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, Trento, Italy; Graduate School Experimental Plant Sciences, Wageningen University, AJ Wageningen, Netherlands; IRTA. Centre de Recerca en Agrigenómica CSIC-IRTA-UAB, Campus UAB-UB – Edifici CRAG, Beellaterra (Cerdanyola del Vallés), Barcelona, Spain
ASSIsT funding source(s)
This work has been co-funded by the EU seventh Framework Programme by the FruitBreedomics project N°. 265582: Integrated Approach for increasing breeding efficiency in fruit tree crops.

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