Sharing our new tool for drawing maps/diagrams of mitochondrial genomes. Can be used with with existing sequences (e.g. GenBank records), or de novo assemblies as part of a mitogenomics pipeline. Runs on Windows, Linux and Mac.
Simon J Goodman, Ian M Carr, Drawing mitochondrial genomes with circularMT, Bioinformatics, Volume 40, Issue 7, July 2024, btae450, https://doi.org/10.1093/bioinformatics/btae450
The app has a graphical user interface allowing full customisation of the map appearance, plus a command line version for batch processing of multiple files. Draws circular and linear maps, and output publication quality image files. Input a wide variety of file formats including from assembly/annotation pipelines such as MITOS.
Both applications are implemented in C#, with binaries, source code and full user guides available on GitHub (https://github.com/msjimc/circularMT). An archive of the published version is available on Zenodo (https://zenodo.org/records/10912319). Linux & Mac versions run under WINE, full instructions given.
Will it work correctly with plant mitochondrial genomes?
One possible problem is that mitochondrial genomes of plants have trans-splicing.
We tested it with animal mt genomes. The input is based on standard text file formats such as .gb, .gff, .mitos etc. It will draw features based on whatever is in the file, but you have full control to select/deselect individual or groups of features. Try it with your data - any glitches let us know.
Thanks, I will share this with my fungal team and see how they like it.