MiniTV

Alignment viewer using AliTV.

Setup

$ git clone https://github.com/weigelworld/minitv
$ python3 -m virtualenv .minitv-venv
$ source .minitv-venv/bin/activate
$ pip install minitv/

minimap2 must be in your PATH for minitv to run. Either install it globally or download the binary from the GitHub repository and copy it into .minitv-venv/bin.

Usage

minitv --aligner_args "-x asm5 -g 150" --no_tree -a test_data/ACD6/TAIR10.gff3 -a test_data/ACD6/Col-0.gff3 -a test_data/ACD6/KBS-Mac-74.gff3 -a test_data/ACD6/Kn-0.gff3 -a test_data/ACD6/Ty-1.gff3 test_data/ACD6/TAIR10.fa test_data/ACD6/Col-0.fa test_data/ACD6/KBS-Mac-74.fa test_data/ACD6/Kn-0.fa test_data/ACD6/Ty-1.fa > out.alitv.json

The resulting out.alitv.json file can be loaded into any AliTV instance, such as this demo site, by going to the "Import and Export" tab and clicking the "Load JSON" button.