Next-generation sequencing has revolutionised the detection of pathogenic variants in people with rare genetic conditions. However, the underlying pathogenic variant in approximately 50% of patients is not resolved with short-read sequencing data. It has been suggested that many of these cases are due to large-scale structural rearrangements, which are more difficult to detect compared to SNVs or small indels when using short-read data. To overcome this problem, long-read sequencing data generated by PacBio or ONT sequencers has been increasingly used in the hope of identifying these large-scale rearrangements.
Once generated, the data is typically aligned to the appropriate genome using a long-read-specific aligner such as minimap2 (GitHub, paper) or lra (GitHub, paper). Once aligned, the data is typically visualised with an application such as IGV Genome Browser (https://www.igv.org/) to identify breakpoints; unfortunately, these programs are limited in their ability to allow the rapid detection and annotation of structural rearrangements; consequently, we have developed AgileStructure specifically for this purpose.
The AgileStructure guide is here:
AgileStructure can be run on most POSIX like systems using Intel or AMD CPUs via WINE whose installation is covered here
The compiled program can be downloaded from here
A static release linked to the Bioinformatics paper is here.
Lascelles, C., Raynor, M., Crinnion, L.A., Rose, A.M., Diggle, C.P., Poulter, J.A., Watson, C.M. and Carr, I.M., 2026. Utilization of long-read sequencing for the detection of structural rearrangements with AgileStructure. Bioinformatics, 42(5), p.btag294.