v0.2.0

mpox-seek

New feature: plot coverage along the genome.

Added a new option called, --plot-coverage, to create per-sample coverage plots along the amplified region of the genome.

• Updated the docker image and conda environment for new required dependencies: deeptools, samtools, and pygenometracks.
  • To use this verion of the pipeline, please re-build or create a new conda environment using the following conda environment file.
• Added new rules to convert BAM to BigWig using deeptools bamCoverage and visualizing the coverage with pygenometracks (from the authors of DeepTools).

Full Changelog: v0.1.0...v0.2.0

v0.1.0

mpox-seek

First release (v0.1.0)

This is the first release of the rapid monekypox pipeline!

Notable features
The pipeline will rapidly build a phylogenetic tree for a set of targeted ONT monkeypox samples data using porechop, minimap2, viral_consensus, mafft, and raxml-ng.

Additional monkeypox strains can be added to the tree, via the --additional-strains option. The --batch-id option can be provided to ensure unique output files are not over-written between runs of the pipeline. When this option is provided, a sub-directory is created in the project folder for writing project-level output files, i.e {output_directory}/project/{batch_id}. The --bootstrap-trees option can be provided to transfer branch supports, calculated by bootstrapping, onto the best scoring tree.

Conda/mamba or singularity can be used to satisfy any software dependencies. The pipeline's reference files are bundled within the github repository. For ease of setup or general use, we recommend using conda/mamba as it is easier to install than singularity. Windows users should use WSL to setup, install, and run the pipeline in a unix-like environment.

Full Changelog: https://github.com/OpenOmics/mpox-seek/commits/v0.1.0