Tersect: a set theoretical utility for exploring sequence variant data

Abstract

Summary Comparing genomic features among a large panel of individuals across the same species is considered nowadays a core part of the bioinformatics analyses. This typically involves a series of complex theoretical expressions to compare, intersect, extract symmetric differences between individuals within a large set of genotypes. Several publically available tools are capable of performing such tasks; however, due to the sheer size of variants being queried, such tasks can be computationally expensive with a runtime ranging from few minutes up to several hours depending on the dataset size. This makes existing tools unsuitable for interactive data query or as part of genomic data visualization platforms such as genome browsers. Tersect is a lightweight, high-performance command-line utility which interprets and applies flexible set theoretical expressions to sets of sequence variant data. It can be used both for interactive data exploration and as part of a larger pipeline thanks to its highly optimized storage and indexing algorithms for variant data. Availability and implementation Tersect was implemented in C and released under the MIT license. Tersect is freely available at https://github.com/tomkurowski/tersect. Supplementary information Supplementary data are available at Bioinformatics online.

A chromosome-level genome assembly ofSolanum chilense, a tomato wild relative associated with resistance to salinity and drought

“…These protein variants were reverse translated back to SNPs, based on the protein MAFFT alignments and the nucleotide sequences of the genes from Augustus and ITAG4.1. Tersect, a tool to perform set operations on variant data [66], intersected the resulting SNPs with the 84 publicly available re- sequenced genomes of 12 tomato species [67]. In order to analyse fixed changes in each species, only homozygous variants were considered, which eliminated 5 genes from the total number.…”

Genes involved in auxin biosynthesis, transport and signalling underlie the extreme adventitious root phenotype of the tomato aer mutant

“…With two flanking markers, F 2 lines carrying aer alleles on chromosome 4 were selected and produced significantly increased number of ARs when carrying the mutant SBRL allele. A multiple genome comparison using the Tersect pipeline (Kurowski and Mohareb 2020 ) in the region between 6.7 and 63.3 Mbp on chromosome 4 (SL4.0) showed high homology between S. pimpinellifolium and aer , which was not the case for most of the aer genome (Figure S8 ). Although there is no evidence that S. pimpinellifolium produces more ARs than AC or other cultivar lines, it definitely has a higher LR initiation capacity than certain cultivars (Alaguero-Cordovilla et al 2018 ), which could contribute to the increased RSA of aer (Fig.…”

A chromosome-level genome assembly of Solanum chilense, a tomato wild relative associated with resistance to salinity and drought

“…These protein variants were reverse translated back to SNPs, based on the protein MAFFT alignments and the nucleotide sequences of the genes from Augustus and ITAG4.1. Tersect, a tool to perform set operations on variant data (Kurowski and Mohareb, 2020), intersected the resulting SNPs with the 84 publicly available re-sequenced genomes of 12 tomato species (100 Tomato Genome Sequencing Consortium et al, 2014). In order to analyse fixed changes in each species, only homozygous variants were considered, which eliminated five genes from the total number.…”