** minidot

[[etc/header.png]]

Quickly produce pretty dotplots from [[https://github.com/lh3/minimap][minimap]] mappings using R/ggplot2.

**** Dependencies

• R packages: ggplot2, stringr, scales, argparse
• curl, gzip (for samples only)

**** Install #+BEGIN_SRC git clone https://github.com/thackl/minidot.git #+END_SRC

**** Samples #+BEGIN_SRC make sample-prochlorococcus make sample-arabidopsis #+END_SRC

Make sample commands will download required data, set up minimap (if not already in $PATH) and run minidot.

***** Prochlorococcus ecotypes #+BEGIN_SRC

actual minidot command invoked by make sample-prochlorococcus after setting up the data

minidot -s -o prochlorococcus.pdf MED4.da SB.fa NATLA2.fa LG.fa MIT9313.fa #+END_SRC

Quickly compare genome organization among multiple bacterial genomes (finished and draft).

[[etc/prochlorococcus.png]]

***** /A. thaliana/ vs /A. lyrata/ - compare two related eukaryotes #+BEGIN_SRC

actual minidot command invoked by make sample-arabidopsis after setting up the data

minidot -o arabidopsis.pdf A.lyrata.fa A.thaliana.fa #+END_SRC

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.