{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,8]],"date-time":"2026-03-08T08:47:54Z","timestamp":1772959674652,"version":"3.50.1"},"reference-count":6,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":423,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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\u00ae (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\u2013trait association analysis. ASSIsT is developed in Python and runs in Windows and Linux.<\/jats:p>\n               <jats:p>Availability and implementation: The software, example data sets and tutorials are freely available at http:\/\/compbiotoolbox.fmach.it\/assist\/.<\/jats:p>\n               <jats:p>Contact: \u00a0eric.vandeweg@wur.nl<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv446","type":"journal-article","created":{"date-parts":[[2015,8,7]],"date-time":"2015-08-07T00:09:48Z","timestamp":1438906188000},"page":"3873-3874","source":"Crossref","is-referenced-by-count":52,"title":["ASSIsT: an automatic SNP scoring tool for in- and outbreeding species"],"prefix":"10.1093","volume":"31","author":[{"given":"Mario","family":"Di Guardo","sequence":"first","affiliation":[{"name":"1 Wageningen UR Plant Breeding, 6700 AA Wageningen, The Netherlands,"},{"name":"2 Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy,"},{"name":"3 Graduate School Experimental Plant Sciences, Wageningen University, 6700 AJ Wageningen, The Netherlands and"}]},{"given":"Diego","family":"Micheletti","sequence":"additional","affiliation":[{"name":"2 Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy,"},{"name":"1 Wageningen UR Plant Breeding, 6700 AA Wageningen, The Netherlands,"}]},{"given":"Luca","family":"Bianco","sequence":"additional","affiliation":[{"name":"2 Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy,"}]},{"given":"Herma J. J.","family":"Koehorst-van Putten","sequence":"additional","affiliation":[{"name":"1 Wageningen UR Plant Breeding, 6700 AA Wageningen, The Netherlands,"}]},{"given":"Sara","family":"Longhi","sequence":"additional","affiliation":[{"name":"1 Wageningen UR Plant Breeding, 6700 AA Wageningen, The Netherlands,"}]},{"given":"Fabrizio","family":"Costa","sequence":"additional","affiliation":[{"name":"2 Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy,"}]},{"given":"Maria J.","family":"Aranzana","sequence":"additional","affiliation":[{"name":"4 IRTA, Centre de Recerca en Agrigen\u00f3mica CSIC-IRTA-UAB, Beellaterra (Cerdanyola del Vall\u00e9s), 08193 Barcelona, Spain"}]},{"given":"Riccardo","family":"Velasco","sequence":"additional","affiliation":[{"name":"2 Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy,"}]},{"given":"Pere","family":"Ar\u00fas","sequence":"additional","affiliation":[{"name":"4 IRTA, Centre de Recerca en Agrigen\u00f3mica CSIC-IRTA-UAB, Beellaterra (Cerdanyola del Vall\u00e9s), 08193 Barcelona, Spain"}]},{"given":"Michela","family":"Troggio","sequence":"additional","affiliation":[{"name":"2 Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy,"}]},{"given":"Eric W.","family":"van de Weg","sequence":"additional","affiliation":[{"name":"1 Wageningen UR Plant Breeding, 6700 AA Wageningen, The Netherlands,"}]}],"member":"286","published-online":{"date-parts":[[2015,8,6]]},"reference":[{"key":"2023020202402640500_btv446-B1","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1186\/s12864-015-1310-1","article-title":"Development and preliminary evaluation of a 90K Axiom\u00ae SNP array in the allo-octoploid cultivated strawberry Fragaria\u2009\u00d7\u2009ananassa","volume":"16","author":"Bassil","year":"2015","journal-title":"BMC Genomics"},{"key":"2023020202402640500_btv446-B2","doi-asserted-by":"crossref","first-page":"e110377","DOI":"10.1371\/journal.pone.0110377","article-title":"Development and validation of a 20K single nucleotide polymorphism (SNP) whole genome genotyping array for apple (Malus\u2009\u00d7\u2009domestica Borkh)","volume":"9","author":"Bianco","year":"2014","journal-title":"PLoS One"},{"key":"2023020202402640500_btv446-B3","doi-asserted-by":"crossref","first-page":"1681","DOI":"10.1534\/g3.114.011023","article-title":"Fast and cost-effective genetic mapping in apple using next-generation sequencing","volume":"4","author":"Gardner","year":"2014","journal-title":"G3"},{"key":"2023020202402640500_btv446-B4","author":"Kermani","year":"2006"},{"key":"2023020202402640500_btv446-B5","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1007\/s11295-013-0679-8","article-title":"\u2018Schmidt\u2019s Antonovka\u2019 is identical to \u2018Common Antonovka\u2019, an apple cultivar widely used in Russia in the breeding for biotic and abiotic stresses","volume":"10","author":"Pikunova","year":"2014","journal-title":"Tree Genet. 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