Contents

# GENOMER-VIEW-AGP 1

## NAME

genomer-view-agp(1) -- Generate agp file views of scaffold

## SYNOPSIS

`genomer view agp`

## DESCRIPTION

**Genomer-view-agp** produces an AGP view of a scaffold. This format shows the 
positions of gaps and contigs in the scaffold. More details on this format can
be found on the [AGP specification page](http://www.ncbi.nlm.nih.gov/projects/genome/assembly/agp/AGP_Specification.shtml "AGP Specification").

This command converts the scaffold into AGP format as follows:

  * contigs:
    Contiguous sequences of non-N nucleotides generate corresponding sequence 
    entries in the AGP file. Note: two sequence positioned next to each other 
    in the scaffold file do not however produce a single contig entry.

  * internal contig gaps:

    Regions of N characters in scaffold sequences are converted 'scaffold' gaps
    in the AGP file. The 'Linkage Evidence' field is set to "internal" and this
    should be set to the correct AGP field type after generation. See the AGP
    Specification for allowed evidence types.

  * unresolved regions:

    'Unresolved' entries in the 'scaffold.yml' file result in a **scaffold**
    gap entry in AGP file. The 'Linkage Evidence' field is set to "specified"
    and this should be set to the correct AGP field type after generation. See
    the AGP Specification for allowed evidence types.

## EXAMPLES

    $ genomer view agp

## BUGS

**Genomer-view** is written in Ruby and depends on the genomer gem. See the 
Gemfile in the genomer-plugin-view gem install directory for version details.

## COPYRIGHT

**Genomer** is Copyright (C) 2012 Michael Barton <http://michaelbarton.me.uk>

Version data entries

4 entries across 4 versions & 1 rubygems

Version	Path
genomer-plugin-view-0.1.0	man/genomer-view-agp.ronn
genomer-plugin-view-0.0.7	man/genomer-view-agp.ronn
genomer-plugin-view-0.0.6	man/genomer-view-agp.ronn
genomer-plugin-view-0.0.5	man/genomer-view-agp.ronn