RT Journal Article
SR Electronic
T1 Verification of <em>Arabidopsis</em> stock collections using SNPmatch - an algorithm for genotyping high-plexed samples
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 109520
DO 10.1101/109520
A1 Pisupati, Rahul
A1 Reichardt, Ilka
A1 Seren, Ümit
A1 Korte, Pamela
A1 Nizhynska, Viktoria
A1 Kerdaffrec, Envel
A1 Uzunova, Kristina
A1 Rabanal, Fernando
A1 Filiault, Daniele
A1 Nordborg, Magnus
YR 2017
UL http://biorxiv.org/content/early/2017/02/17/109520.abstract
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