Smithsonian Targeted Enrichment Workshop - In Review

Posted March 31, 2016 - 1:58pm

On March 15th, the Smithsonian Institute for Biodiversity Genomics (SIBG) Bioinformatics Group hosted an all-day target enrichment/bait capture workshop. This workshop was geared toward researchers who currently use or would like to use target capture techniques and data in their research.

Paul Frandsen (ORIS/OCIO) offered a short Hydra training workshop on Monday March 14th. This two-hour training provided a short introduction to Hydra, which helped prepare participants for the exercises given during the targeted enrichment workshop.

The workshop started with an introductory lecture on March 15th by Alison Devault (MYcroarray): Planning a Successful Target Enrichment Project with MYbaits

Lily Parker (CCEG, GMU) presented on CCEG's use of Target Enrichment/Bait Capture.

In the afternoon, the SIBG Bioinformatics Group ran a "hands-on" workshop, covering:

  • Post Processing of Target Enrichment data
  • Phyluce pipeline on SI Hydra HPC (Faircloth BC. 2015. PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics.)
  • The Phyluce package now includes a number of tools spanning: 1) the assembly of raw read data to contigs, 2) the identification of UCE contigs, 3) parallel alignment generation, alignment trimming, and alignment data summary methods in preparation for analysis, 4) alignment and SNP calling using UCE or other types of raw-read data.