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README.md

Summary: metrics for genome projects

About

Summary is a plugin for the genomer tool for genome finishing. This summary plugin provides metrics that useful are to understanding that state of your genome scaffold. Plugins are added to a genomer project by specifying them in the project Gemfile. Each summary function is documented with a manual page.

Usage

The following command will provide a list of all the gaps in your genome scaffold:

$ genomer summary gaps

Producing output similiar to as follows:

+----------+----------+----------+----------+--------------+
|                      Scaffold Gaps                       |
+----------+----------+----------+----------+--------------+
|  Number  |  Length  |  Start   |   End    |     Type     |
+----------+----------+----------+----------+--------------+
|        1 |      400 |   121250 |   121649 |  unresolved  |
|        2 |      659 |   123354 |   124012 |    contig    |
|        3 |       10 |   126781 |   126790 |  unresolved  |
|        4 |       10 |   127393 |   127402 |  unresolved  |
|        5 |      500 |   778936 |   779435 |  unresolved  |
|        6 |      659 |   781140 |   781798 |    contig    |
|        7 |       10 |   784567 |   784576 |  unresolved  |
|        8 |      300 |   785179 |   785478 |  unresolved  |
|        9 |      556 |   803968 |   804523 |    contig    |
|       10 |      242 |  1032294 |  1032535 |    contig    |
|       11 |     1751 |  1057108 |  1058858 |    contig    |
|       12 |      575 |  1137194 |  1137768 |    contig    |
<remainder omitted>

Other commands are available for showing contigs, sequences, and the complete scaffolded genome. These are listed in the manual page directory.

Installation

Add this line to your genomer projects's Gemfile:

gem 'genomer-plugin-summary'

And then execute in the project directory:

$ bundle

Run the help command and the summary plugin should be available:

$ genomer help
$ genomer man summary

Copyright

Genomer copyright (c) 2010 by Michael Barton. Genomer is licensed under the MIT license. See LICENSE.txt for further details. The tape measure image is used under a Creative Commons Generic 2.0 Licence. The original can be found on flickr.

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