PT  - JOURNAL ARTICLE
AU  - Pisupati, Rahul
AU  - Reichardt, Ilka
AU  - Seren, Ümit
AU  - Korte, Pamela
AU  - Nizhynska, Viktoria
AU  - Kerdaffrec, Envel
AU  - Uzunova, Kristina
AU  - Rabanal, Fernando
AU  - Filiault, Daniele
AU  - Nordborg, Magnus
TI  - Verification of <em>Arabidopsis</em> stock collections using SNPmatch - an algorithm for genotyping high-plexed samples
AID  - 10.1101/109520
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 109520
4099  - http://biorxiv.org/content/early/2017/02/17/109520.short
4100  - http://biorxiv.org/content/early/2017/02/17/109520.full
AB  - Large-scale studies such as the ​Arabidopsis thaliana 1001 Genomes Project aim to understand genetic variation in populations and link it to phenotypic variation. Such studies require routine genotyping of stocks to avoid sample contamination and mix-ups. To genotype samples efficiently and economically, sequencing must be inexpensive a​nd data processing simple. Here we present SNPmatch, a tool which identifies the most likely strain (inbred line, or “accession”) from a SNP database. We tested the tool by performing low-coverage sequencing of over 2000 strains. SNPmatch could readily genotype samples correctly from 1-fold coverage sequencing data, and could also identify the parents of F1 or F2 individuals. SNPmatch can be run either on the command line or through AraGeno (https://arageno.gmi.oeaw.ac.at), a web interface that permits sample genotyping from a user-uploaded VCF or BED file.Availability and implementation: https://github.com/Gregor-Mendel-Institute/SNPmatch.git