An R package providing tools for visualization and automatic detection of complex, NAHR-driven rearrangements (few kbp to multiple Mbp) using genome assemblies. Modules include:

• Liftover of coordinates between arbitrary human DNA assemblies
• Accurate sequence alignments of multi-MB DNA sequences
• Dotplot visualizations
• Segmented Dotplots
• A tree-based caller for complex, nested NAHR-mediated rearrangements.

NAHRwhals requires installed versions of:

• minimap2 (link)
• bedtools (link)
• gawk (link)
• R >= 4.1.0

Make sure minimap2, bedtools and gawk are installed on your system. (It is sufficient if you have access to working binaries).

git clone https://github.com/WHops/NAHRwhals.git
cd NAHRwhals
git checkout main

You can install with the following command, which uses devtools::install to resolve R dependencies. This typically takes a few minutes. (Consider running in a new conda environment)

Rscript install_package.R

Confirm successful installation using

R
> library(nahrwhals)
> quit()

NAHRwhals internally calls minimap2 and bedtools. Specify your paths to the binaries in conf/conf_default.txt and conf/conf_fa2fa.txt.

Typically, you can find the binaries using:

which bedtools
> /your/path/to/bedtools
which minimap2
> /your/path/to/minimap2

Edit the config files as follows:

minimap2_bin = '/your/path/to/minimap2'
bedtools_bin = '/your/path/to/bedtools'

To confirm that NAHRwhals has been correctly installed, run a testrun which should produce output files and plots in the ./res folder:

Rscript nahrwhals.R --config conf/conf_default.txt

NAHRwhals can also skip the initial search for sub-sequences, and call SVs directly on two regional fasta files by setting `compare_full_fastas = TRUE'. Run an example via:

Rscript nahrwhals.R --config conf/conf_fa2fa.txt

To run your own data, exchange genome_x_fa (typically a reference, e.g. hg38), genome_y_fa (typically a genome assembly) and your coordinates of interest (seqname_x, start_x, end_x) in the config file.

Parameters in the config file can be overwritten from the commandline, e.g. to add a gene annotation track to the plots:

Rscript nahrwhals.R --config conf/config_examplerun.txt --params anntrack='testdata/assemblies/hg38_partial_genes.bed'

NAHRwhals is still in development, and errors in usage are to be expected. Please help improve the code by reporting issues you encounter.

If you find NAHRwhals useful, please cite:

https://www.biorxiv.org/content/10.1101/2023.03.09.531868v1

Please direct any correspondence to: Wolfram Höps ([email protected])