Contents

# GENOMER-VIEW-FASTA 1

## NAME

genomer-view-fasta(1) -- Generate fasta view of scaffold

## SYNOPSIS

`genomer view fasta <--contigs> [...<header-options>]`

## DESCRIPTION

**Genomer-view-fasta** produces an fasta file of scaffold. This format provides
the complete scaffolded sequence of all contigs and gaps specified in the
**scaffold.yml** file.

  **--contigs**:

  Instead of generating a single sequence where gaps are represented by
  N-filled regions generate a fasta file where each contiguous region of
  sequence is a new fasta entry. Gap regions are not included in the fasta
  file. This option is useful if submitting an incomplete genome sequence to
  GenBank as the contigs are require in addition to an AGP file (see
  genomer-view-agp(1)).

Additional header options can be specified. These are useful for adding
metadata to the fasta sequence. Any combination of dashes (-) and characters
may be used. See the example below for how this may be used.

## EXAMPLES

    genomer view fasta	                      				 \
      --contigs                                        \
      --organism='Pseudomonas fluorescens'             \
      --strain='R124'                                  \
      --gcode='11'                                     \
      --isolation-source='Orthoquartzite Cave Surface' \
      --collection-date='17-Oct-2007'                  \
      --completeness='Complete'                        \

## 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-fasta.ronn
genomer-plugin-view-0.0.7	man/genomer-view-fasta.ronn
genomer-plugin-view-0.0.6	man/genomer-view-fasta.ronn
genomer-plugin-view-0.0.5	man/genomer-view-fasta.ronn