https://github.com/msjimc/circularMT
https://github.com/msjimc/circularMT
Last synced: 7 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/msjimc/circularMT
- Owner: msjimc
- Created: 2024-02-29T18:34:27.000Z (over 2 years ago)
- Default Branch: master
- Last Pushed: 2025-06-09T16:23:28.000Z (about 1 year ago)
- Last Synced: 2025-06-09T17:31:53.220Z (about 1 year ago)
- Language: C#
- Size: 25 MB
- Stars: 10
- Watchers: 2
- Forks: 0
- Open Issues: 1
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Metadata Files:
- Readme: README.md
Awesome Lists containing this project
- awesome-genome-visualization - circularMT - genome-visualization/circularmt.png) (Circular)
README
# circularMT
### Command line version
This application is designed as a desktop application, however, a command line console version is available [here](https://github.com/msjimc/circularMT/tree/ddfd7039e0ca9e12ff99396b319034f22ec7c4dd/circularMT-console). The command line version creates the same type of images as ```circularMT```, but is less flexible. It is assumed ```circularMT-console``` will be used as part of a generic pipeline, while ```circularMT``` will be used to create images for papers or theses etc.
## Contents
- [Introduction](#Introduction)
- [Guide](#guide)
- [Download](#download)
- [Running on Linux systems](#running-on-linux-systems)
- [Citation](#citation)
## Introduction
```circularMT``` is designed to create images of the genomic organisation of mitochondrial genomes that can be used to display the arrangement of the genes they encode. Images can be exported as 300 dpi TIFF, bitmap, PNG or JPEG files for use in reports, publications or a thesis. The maps can be circular like the one to the right or linear like the one below.
The data can be imported from a wide range of file formats such as *.fasta, *.mitos, *.gb, *.bed, *.seq, *.gtf and *.gff files. While ```circularMT``` can process these files, *.fasta and *.bed files in particular most conform to a set format not present in all files.
Once imported the resultant image can be rotated, the strands switched around and the features renamed, deleted and colour scheme changed to obtain the desired map.
## Guide
The user guide is [here](Guide/README.md).
## Download
The prebuilt program can be downloaded [here](Program/README.md).
## Running on Linux systems
The prebuilt programs can be run on Linux (and macOS) using the Wine package as described [here](Linux_with_Wine/README.md).
## Citation
Goodman SJ, Carr IM.
[Drawing mitochondrial genomes with circularMT.](https://academic.oup.com/bioinformatics/article/40/7/btae450/7713370)
Bioinformatics. 2024 Jul 13;40(7):btae450.
doi: 10.1093/bioinformatics/btae450.
## Zenodo archive
An archived version of the first release is available from here:
[](https://doi.org/10.5281/zenodo.10912319)