https://github.com/thackl/minidot

Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2
https://github.com/thackl/minidot

Last synced: 4 months ago
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Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2

• Host: GitHub
• URL: https://github.com/thackl/minidot
• Owner: thackl
• License: mit
• Created: 2016-06-23T03:13:08.000Z (about 8 years ago)
• Default Branch: master
• Last Pushed: 2016-08-30T13:53:07.000Z (almost 8 years ago)
• Last Synced: 2024-01-17T03:18:16.638Z (6 months ago)
• Language: R
• Homepage:
• Size: 991 KB
• Stars: 67
• Watchers: 5
• Forks: 10
• Open Issues: 5
• Metadata Files:
  • Readme: README.org
  • License: LICENSE

Lists

• repo-5916-awesome-genome-visualization - Minidot - genome-visualization/minidot.png) (Dotplot)
• awesome-genome-visualization - Minidot

README

        
** 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.