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GenomicsAotearoa / long-read-assembly

Long-read assembly workshop
https://genomicsaotearoa.github.io/long-read-assembly/
GNU General Public License v3.0
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MashMap with generateDotPlot #7

Closed DininduSenanayake closed 1 year ago

DininduSenanayake commented 1 year ago

MashMap module with generateDotPlot

DininduSenanayake commented 1 year ago 
$ module load MashMap/3.0.4-Miniconda3

$ $ mashmap --help
-----------------
Mashmap is an approximate long read or contig mapper based on Jaccard
similarity
-----------------
$ module load MashMap/3.0.4-Miniconda3

$ generateDotPlot 

  USAGE: generateDotPlot <terminal> <size> <mashmap ouptut file>

  DESCRIPTION:
    generateDotPlot generates plots of mapping data produced by mashmap (or similar 
    formatted mapping output). This script borrows most of the routines from 
    mummerplot in Mummer3 software package. For showing the output plut, either
    an x11 window will be spawned or an output file (.ps or .png) will be 
    generated. This script has a dependency on gnuplot.

  MANDATORY:
    <terminal>              Set the output terminal to either 'x11', 'postscript' or 'png'

    <size>                  Set the output size to either 'small', 'medium' or 'large'

    <mashmap output file>   Provide the mapping output file generated by mashmap