HYBRIDCHECK: software for the rapid detection, visualization and dating of recombinant blocks in genome sequence data

Benjamin Ward and Cock van Oosterhout

University of East Anglia, Norwich Research Park, Norwich, UK

email: Ben.Ward@sainsbury-laboratory.ac.uk and c.van-oosterhout@uea.ac.uk

HYBRIDCHECK (Hybridisation, Recombination, Introgression, Dating Software) is a bioinformatics tool designed to visualize the signal of recombination (and genetic introgression) in DNA sequence data present in large (multiple kb) contigs and whole genome sequence data of three or more individuals.It reports several summary statistics of these events, including breakpoint positions, number of SNPs, and it estimates the age of the recombination event. HYBRIDCHECK can also be applied to analyse smaller amplicons (1kb), as well as high density SNP data.Its primary use is to inform users about the prevalence of recombination, visualize the recombination blocks and the mosaic-like genome structure, calculate the divergence time of each block, and hence, date the age of each recombination event.

HYBRIDCHECK has a user-interface, and it is simple and relatively fast to run. The output of HYBRIDCHECK aims to direct the user to more computationally-intensive phylogenetic and population genetic analyses, e.g. to confirm the recombination events with multiple algorithms present in RDP3 (Martin et al. 2010), and/or date the divergence of the recombination blocks in a Bayesian framework, e.g. in BEAST (Drummond et al. 2012).

The analysis with HYBRIDCHECK consists of the following three-steps:

  1. Load nucleotide data in FASTA format into the R environment using the user interface.
  2. Analyse the sequence similarity of all possible sequence triplets with a sliding window approach.
  3. HYBRIDCHECK detects recombination blocks and calculates summary statistics for each recombination block (i.e. number of SNPs, breakpoint positions, length of recombination block, the probability that sequence similarity is caused by mutations rather than by recombination). HYBRIDCHECK also draws graphs of contigs illustrating the location of recombination blocks relative to base position, and it estimates the mean (5-95%CI) coalescence time of each recombination block, and it thereby dates each recombination event.Click here to visit the site and code repository that is curated by the team. It will be the most up to date with improvements and bugfixes in the future.

The three links below link directly to the most up to date versions of the software in the HYBRIDCHECK repository.

OSX: http://ward9250.github.io/HybridCheck/Installers/OSX/HybridCheck.app.zip

Windows: http://ward9250.github.io/HybridCheck/Installers/Windows/HybridCheckInstaller.EXE

Linux: http://ward9250.github.io/HybridCheck/Installers/Linux/HybridCheck_Linux_Installer.zip

It is recommended that new users follow the instructions on how to install from the R console, and also with Docker at this link:  http://ward9250.github.io/HybridCheck/use_HybridCheck.html

When using HYBRIDCHECK please cite:

Ward BJ, van Oosterhout C. 2016 HYBRIDCHECK: software for the rapid detection, visualization and dating of recombinant regions in genome sequence data. Mol Ecol Resour. Mar;16(2):534-9.

Earlham institute
Quadram Institute Bioscience
John Innes Centre
The Sainsbury Laboratory
University of East Anglia

© Norwich Research Park Science 2019. All rights reserved