Geneious Software and LIMS Plugin

This GitHub repository hosts the materials used in the Smithsonian Institution workshop: Geneious Software and LIMS Plugin

The purpose of the workshop is to provide intensive training for Geneious software and the associated LIMS plugin. We will be demonstrating the pipeline that CBOL developed for SI Barcode Network projects, but we are opening it to the entire Smithsonian community. We will show how any Sanger sequencing project can use the same system to organize their lab workflows and data.

Resources

Everything we covered in class (and more) is covered in the SI Barcode Network Informatics ReadTheDocs page here: SIBarcodeNetwork.rtfd.org

The Moorea Biocode LIMS Wiki page contains the official documentation for the Geneious Biocode Plug-in, and can be found here: software.mooreabiocode.org

The Smithsonian provides a floating institutional license for 25 concurrent users. You can find instructions for how to connect to this floating license here: http://darwin.si.edu/about/LAB%20Documents/Geneious%20and%20Sequencher%20install.pdf. Note: This is a Smithsonian Intranet site, so you can only connect to it on a Smithsonian network.

Class Materials

Slides, in-class materials, and links to recordings can be found in each Session folder.

[Session 1](Session\ 1) (July 12, 2016):

• Introduction to DNA Barcoding pipeline
• DNA Barcode Data Standard
• FIMS and spreadsheet validation
• Geneious layout introduction

[Session 2](Session\ 2) (July 13, 2016):

• Logging into Geneious Biocode Plugin
• Naming conventions in FIMS and LIMS
• Creating extraction plates
• Searching in LIMS
• Creating PCR plates

[Session 3](Session\ 3) (July 19, 2016):

• Revisit generating PCR plates, primers, thermocycling protocols
• Uploading and scoring gel images
• Generating cycle sequencing plates
• Attaching raw traces to plates (including sequence naming convention)
• Downloading traces to local

[Session 4](Session\ 4) (July 20, 2016):

• Assembling contigs
• Binning parameters
• Quality control / Sequence Analyses

[Session 5](Session\ 5) (July 26, 2016):

• Marking sequences as Pass or Fail in LIMS
• Annotating with FIMS/LIMS data
• GenBank Upload