** minidot
[[etc/header.png]]
Quickly produce pretty dotplots from [[https://github.com/lh3/minimap][minimap]] mappings using R/ggplot2.
**** Dependencies
**** Install
git clone https://github.com/thackl/minidot.git
**** Samples
make sample-prochlorococcus make sample-arabidopsis
Make sample commands will download required data, set up minimap (if not already in $PATH) and run minidot.
***** Prochlorococcus ecotypes
minidot -s -o prochlorococcus.pdf MED4.da SB.fa NATLA2.fa LG.fa MIT9313.fa
Quickly compare genome organization among multiple bacterial genomes (finished and draft).
[[etc/prochlorococcus.png]]
***** /A. thaliana/ vs /A. lyrata/ - compare two related eukaryotes
minidot -o arabidopsis.pdf A.lyrata.fa A.thaliana.fa
Compare two related eukaryotic genomes. Larger genomes are automatically run in =fast= mode, which is less sensitive and looks only for larger stretches of similarity (>500bp).
For /A.t./ vs /A.l./, mapping & plotting takes about 1.5 minutes (desktop PC, 3 threads, 8GB RAM). That's probably faster than downloading the genomes in the first place...
[[etc/arabidopsis.png]]
**** Contact Any kind of feedback is highly appreciated. Feel free to either report [[https://github.com/thackl/minidot/issues/new][issues]] directly via github or shoot me an email.