Tuesday, 5 February 2013

Fwd: [BioRuby] Genomer: a ruby project to simplify genome finishing

Looks intriguing! anyone else using it? 

---------- Forwarded message ----------
From: Michael Barton <mail AT michaelbarton.me.uk>
Date: Sun, Feb 3, 2013 at 5:34 AM
Subject: [BioRuby] Genomer: a ruby project to simplify genome finishing
To: BioRuby Mailing List

Hi Everyone,

I've been working a sequencing microbial genomes during my current post doc
position. I've combined many of the ruby scripts I was using into a single tool
called "genomer" which might be of interest to other bioinformaticians working
in the same area.

I used this tool to simplify the smaller, mundane tasks associated with a
genome. For instance moving contigs and associated annotations around,
generating the required files to submit to GenBank, and generating summaries of
the genome scaffold.

I created a small screencast for anyone who is interested in finding out more:

I wrote this tool to satisfy my own needs and use genomer extensively for the
microbial genome projects in our lab. My GNU Makefile (http://bit.ly/WMKlCZ)
from a P. fluorescens project illustrates how genomer combined with GenBank's
tbl2asn can be used to build the all files required for genome submission.

Hopefully genomer may be useful to other bioinformaticians and simplify the
steps required to finish and submit a genome.


Michael Barton

BioRuby Project - http://www.bioruby.org/

I have created an additional screencast to follow up. This provides a more
concrete example of using genomer to generate the files required to submit a
genome project to GenBank.




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