PatchWorkPlot

Docker container for PatchWorkPlot, a tool for visualization of pairwise alignments of multiple sequences as dot plots arranged into an upper or lower triangular matrix.

Citation

Pospelova M, Safonova Y. PatchWorkPlot: simultaneous visualization of local alignments across multiple sequences. Bioinformatics. 2025; btaf504. doi:10.1093/bioinformatics/btaf504.

Container image

docker pull picotainers/patchworkplot:latest

Usage

The image includes PatchWorkPlot and minimap2. For alignment-based runs, explicitly select minimap2:

docker run --rm picotainers/patchworkplot:latest --help
docker run --rm -v "$PWD:$PWD" -w "$PWD" picotainers/patchworkplot:latest \
  -i input_config.csv \
  -o patchwork_output \
  --aligner minimap2

Notes

• The upstream package defaults to lastz, which is not bundled here.
• Use --aligner minimap2 unless you provide custom alignment files.
• Upstream repository: https://github.com/yana-safonova/PatchWorkPlot