ArticleBioinformatics (Oxford, England)2015
ASSIsT: an automatic SNP scoring tool for in- and outbreeding species.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- QTL mapping and genomic prediction of resistance to apple blotch (Molecular breeding : new strategies in plant improvement · 2026Article
- Article
- First genomic insights into the introgression of almond PPV-Marcus resistance into peach.Frontiers in plant science · 2026Article
- AxioSAFE: an accessible, semi-automatic filtering tool for the curation of genotyping datasets.Bioinformatics advances · 2026Article
- Tracing the color: quantitative trait loci analysis reveals new insights into red-flesh pigmentation in apple (Horticulture research · 2024Article
- Why we thrive beneath a northern sky - genomic signals of selection in apple for adaptation to northern Sweden.Heredity · 2024Article
- Towards Marker-Assisted Breeding for Black Rot Bunch Resistance: Identification of a Major QTL in the Grapevine Cultivar 'Merzling'.International journal of molecular sciences · 2023Article
- Genome-wide association analysis ofFrontiers in plant science · 2023Article
- A high-density integrated map for grapevine based on three mapping populations genotyped by the Vitis18K SNP chip.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2022Article
- Genetic Diversity and Genome-Wide Association Study of Morphological and Quality Traits in Peach Using Two Spanish Peach Germplasm Collections.Frontiers in plant science · 2022Article
- Construction of a collection of introgression lines of "Texas" almond DNA fragments in the "Earlygold" peach genetic background.Horticulture research · 2022Article
- Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing.International journal of molecular sciences · 2021Review
- Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls.BMC genomics · 2021Article
- Genetic characterization of an almond germplasm collection and volatilome profiling of raw and roasted kernels.Horticulture research · 2021Article
- Genome-Wide Association Study of Brown Rot (Frontiers in plant science · 2021Article
- RosBREED: bridging the chasm between discovery and application to enable DNA-informed breeding in rosaceous crops.Horticulture research · 2020Review
- The cherry 6+9K SNP array: a cost-effective improvement to the cherry 6K SNP array for genetic studies.Scientific reports · 2020Article
- Unraveling the genetic origin of 'Glera', 'Ribolla Gialla' and other autochthonous grapevine varieties from Friuli Venezia Giulia (northeastern Italy).Scientific reports · 2020Article
- Recommendations for Choosing the Genotyping Method and Best Practices for Quality Control in Crop Genome-Wide Association Studies.Frontiers in genetics · 2020Review
- Genomic prediction of fruit texture and training population optimization towards the application of genomic selection in apple.Horticulture research · 2020Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
unlabelledASSIsT (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: eric.vandeweg@wur.nl.
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