Procedures and data for the iLoci study first described in Standage, Lai, and Brendel (2021; BioRxiv pre-print).

This repository documents application of AEGeAn code to derive, classify, and analyze genomic interval loci (iLoci) as described in the paper Standage, Lai, and Brendel (2021). Please refer to the AEGeAn Installation site for details on how to obtain the relevant software. The simplest way to get going is to use the AEGeAn Singularity container, e.g. as follows:

cd
git clone https://github.com/BrendelGroup/iLoci_SLB22NARGB
cd iLoci_SLB22NARGB/work
wget https://BrendelGroup.org/SingularityHub/aegean.sif
alias rws="singularity exec -e -B ~/iLoci_SLB22NARGB ~/iLoci_SLB21/work/aegean.sif"
rws fidibus -h

In the above example, you clone this repository into your Linux home directory, go into the iLoci_SLB22NARGB/work directory that has been created, download the AEGeAn Singularity container, define the bash alias rws ("run with singularity"), and check that everything works by showing the "help" lines for the AEGeAn command fididbus.

Of course this assumes that you have Apptainer/Singularity installed on your system. Check whether there is package built for your system. Otherwise, follow the instructions to install Singularity from source code.

To reproduce the data discussed in Standage, Lai, and Brendel (2022), go to ./work and follow the instructions in the README file.

Daniel S Standage, Tim Lai, and Volker P Brendel (2022) iLoci: Robust evaluation of genome content and organization for provisional and mature genome assemblies. Nucleic Acids Research Genomics and Bioinformatics, Volume 4, Issue 1, March 2022, lqac013.

Original pre-print: at BioRxiv.

Please direct all comments and suggestions to Volker Brendel at Indiana University.