Standard operating procedures

Ordering and supplies:

• Item and part numbers

Chemicals and solutions:

• Potassium buffered saline (PBS)

• TBE (5X)

General lab protocols:

• Taking care of hibernating (diapausing eggs)

Molecular lab protocols:

• DNA extraction protocol: MagAttract HMW kit

• Pouring and running agarose gels

  • Autoclaving: dry and liquid settings

  • Genotyping-by-sequencing library preparation protocol

  • Download the GBS barcode sequences here

DNA sequencing services:

• UT GSAF

Computer protocols:

• • Using SLURM on the UofU CHPC, wikipage

  • UofU CHPC software and modules

  • General information on the DoRC computer cluster

  • Quick guide to running and submitting jobs on the DoRC cluster with SLURM

• Globus GridFTP for transferring large files

• Useful UNIX commands that I always forget

Analytical protocols:

• Sequence alignment and variant calling

  • GATK help page on required read group fields

  • Best practices for variant calling with GATK (videos)

  • Updated workflow suggested by samtools (note that some steps are probably inappropriate for GBS data).

• Removing barcodes for GBS data and filtering for phiX

• SRA sequence data upload

  • Sam's protocol for genome annotation (for L. melissa)