#17 Implement Annotation Pipeline in Galaxy

[Jay Humphrey]

In a local Galaxy installation, replicate the prediction and annotation pipelines.

[Jay Humphrey]

I am building a how-to over at Wiki:Galaxy

[Lee Katz]

Thanks Jay! I just contacted King to see if he'll be our senior author and
help us actually submit it when the time comes (no response yet). Please
add that the assembly stage should be in Galaxy too.

I was afraid to use the sourceforge wiki because they upgraded or
something. Think it's ok to move all my current documentation to it?

Here is the current list of things to do or that have been done for the
update paper

• Better raw read handling
  • FastQC integration
  • Read trimming/cleaning tool
• Illumina and PacBio assembly (PacBio is a little shakey; I might not
  stress it)
  • Many scripts to aid in assembly: assembly merging tool, read clean
    up, assembly metrics, read metrics, ...
• rRNA prediction
• Abx resistance genes identification - useful in my branch at CDC
  • Hopefully a "resistance determinant locator"
• Multithreading (faster analysis in most cases than the previous
  version)
• CRISPR annotation - useful for PulseNet and others at CDC
• Integration into Galaxy - user friendliness; integration with other
  bioinformatics tools
• Standardized Genbank output files; readily readable by Apollo genome
  browser (or other local genome browser)
• Documentation (currently at
  http://leekatz.com/wiki/index.php?title=Bioinformatics/cgp)
• Probably other things I'm not thinking of

On Fri, Feb 22, 2013 at 6:28 AM, Jay Humphrey jhumphrey6@users.sf.netwrote:

I am building a how-to over at Wiki:Galaxyhttp://sourceforge.net/apps/mediawiki/cg-pipeline/index.php?title=Galaxy

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• [feature-requests:#17]http://sourceforge.net/p/cg-pipeline/feature-requests/17/Implement Annotation Pipeline in Galaxy
  *

Status: open
Created: Fri Feb 22, 2013 11:16 AM UTC by Jay Humphrey
Last Updated: Fri Feb 22, 2013 11:16 AM UTC
Owner: Jay Humphrey

In a local Galaxy installation, replicate the prediction and annotation
pipelines.

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--
Lee Katz, Ph.D.

[Jay Humphrey]

I have just spent a few hours looking at how to import a local file. Next step will be to make a file import tool and use it to import Swissprot and Trembl fasta files to make the prediction blastdb.