# GENOMER-SUMMARY-CONTIGS 1

## NAME

genomer-summary-contigs(1) -- summarise the contigs in the scaffold

## SYNOPSIS

`genomer summary contigs [<--output=csv>]`

## DESCRIPTION

Generates a summary of the contigous sequence used in the scaffolded output
sequence. The output may be generated in CSV format if preferred using the
<--output=csv> option. This summary produces a table with the following
attributes:

  * Contig:

    The number of the contig in the final scaffold. Generated from counting
    each contiguous length of non-N characters from the beginning scaffolded
    sequence.

  * Start:

    The start position of the contig in the final scaffold sequence.

  * End:

    The end position of the contig in the final scaffold sequence.

  * Size (bp):

    The size of the contig in the final scaffold sequence.

  * Size (%):

    The size of the contig in the final scaffold sequence as a percentage of
    the total sequence.

  * GC:

    The G+C content of the contig as percentage the total GCAT length of the
    contig.

## BUGS

**Genomer-summary** is written in Ruby and uses several RubyGem dependencies. 
See the .gemspec file in the install directory for version details.

## COPYRIGHT

**Genomer** is Copyright (C) 2011 Michael Barton <http://michaelbarton.me.uk>