Modern genomics techniques generate overwhelming quantities of data. Extracting population genetic variation demands computationally efficient methods to determine genetic relatedness between individuals (or "samples") in an unbiased manner, preferably de novo. Rapid estimation of genetic relatedness directly from sequencing data has the potential to overcome reference genome bias, and to verify that individuals belong to the correct genetic lineage before conclusions are drawn using mislabelled, or misidentified samples. We present the k-mer Weighted Inner Product (kWIP), an assembly-, and alignment-free estimator of genetic similarity. kWIP combines a probabilistic data structure with a novel metric, the weighted inner product (WIP), to efficiently calculate pairwise similarity between sequencing runs from their k-mer counts. It produces a distance matrix, which can then be further analysed and visualised. Our method does not require prior knowledge of the underlying genomes and applications include establishing sample identity and detecting mix-up, non-obvious genomic variation, and population structure. We show that kWIP can reconstruct the true relatedness between samples from simulated populations. By re-analysing several published datasets we show that our results are consistent with marker-based analyses. kWIP is written in C++, licensed under the GNU GPL, and is available from https://github.com/kdmurray91/kwip.

MOTIVATION: One challenging aspect of genotyping and association mapping projects is often the identification of markers that are informative between groups of individuals and to convert these into genotyping assays. RESULTS: The Multiple SNP Query Tool (MSQT) extracts SNP information from multiple sequence alignments, stores it in a database, provides a web interface to query the database and outputs SNP information in a format directly applicable for SNP-assay design. MSQT was applied to Arabidopsis thaliana sequence data to develop SNP genotyping assays that distinguish a recurrent parent (Col-0) from five other strains. SNPs with intermediate allele frequencies were also identified and developed into markers suitable for efficient genetic mapping among random pairs of wild strains. AVAILABILITY: The source code for MSQT is available at http://msqt.weigelworld.org, together with an online instance of MSQT containing data on 1214 sequenced fragments from 96 ecotypes (wild inbred strains) of the reference plant A. thaliana. All SNP genotyping assays are available in several formats for broad community use. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.