galaxy-pcr-markers
==================

Scripts for design of PCR-based Marker Assays from DNA sequence variant data, and xml wrappers for use in  Galaxy  workflow environment 

Also available for download at Galaxy Toolshed http://toolshed.g2.bx.psu.edu/
hg clone http://toolshed.g2.bx.psu.edu/repos/john-mccallum/pcr_markers

NOTE that the primer design tool *design_primers.py*  relies on EMBOSS ePrimer3 which depends on Primer3 1.1.4.
The updated tool *design_HRM_primers.py* does not have this restriction and should work with Primer3 V2.

Please see development branch HRM for optimised design of high-resolution melting PCR assays using the uMelt web service at University of Utah.


**CITATION**
A Toolkit For Bulk PCR-Based Marker Design From Next-Generation Sequence Data: Application For Development Of A Framework Linkage Map In Bulb Onion (Allium cepa L.) (2012)

Samantha Baldwin, Roopashree Revanna, Susan Thomson, Meeghan Pither-Joyce, Kathryn Wright, Ross Crowhurst, Mark Fiers, Leshi Chen, Richard MacKnight, John A. McCallum

BMC Genomics 2012, 13:637  http://www.biomedcentral.com/1471-2164/13/637/abstract

**Acknowledgements**
Current development of these tools is funded by the New Zealand Ministry for Business, Innovation & Employment project 'Virtual Institute of Statistical Genetics' (VISG)
See http://www.visg.co.nz