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

[Michael Barton]

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.

http://www.youtube.com/watch?v=jVn62pMnIRA&hd=1

Thanks

Mike

On Sat, Feb 02, 2013 at 04:34:30PM -0500, Michael Barton wrote:

> 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: http://youtu.be/HfsdJOELFjs?hd=1
>
> 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.
>
> Thanks
>
> Michael Barton