Donut

just a simple tool that generates a circos plot from a bunch of fasta files

usuage

0. the input files schould be named like $genome_$sample.fasta and the input fasta files should have the following header formt: >contig-$number
1. clone this repo git clone https://github.com/philippmuench/Donut.git
2. put your fasta (one or multipe) files in the data/genomes/ folder
3. add your Hidden Markov model file to data/hmm/model.hmm
4. start the docker container docker run -v /absolute/path/to/data/folder:/data philippmuench/donut
5. inspect the output written to data/output/

example output

from outer to inner:

• GC content
• gene density (black), hypothetical gene density (red)
• match to HMM models against ORFs
• links: similar ORF by blast
• colored links: similar ORFs that cover full a HMM match

development

comment the entrypoint in Dockerfile out than build the docker image from scatch

sudo docker build -t donut .

then start in interactive mode

sudo docker run -it -v /home/pmuench/github.com/philippmuench/easycircos/data:/data donut

inside the docker image start the tool

./start.sh

The error print to screen are not critical, becaused the hmmvis tool tries to export png image to the screen which is not possible within docker.

You can also change data/config/circos.config file from outside the container (because its mounted to the image) and run the circos step only to update the output file

./start_circos.sh