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 Rahul Pisupati
A1 Ilka Reichardt
A1 Ümit Seren
A1 Pamela Korte
A1 Viktoria Nizhynska
A1 Envel Kerdaffrec
A1 Kristina Uzunova
A1 Fernando Rabanal
A1 Daniele Filiault
A1 Magnus Nordborg
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