Tutorial

This tutorial outlines various use cases to illustrate a range of possible applications of the SMAP package.

Each use case is developed by initial download of data, some command line examples, some navigation through directories, creation of custom files, and ilustrated by typical output files, which may be input for the next step in the workflow.

Install and test the SMAP package following these installation instructions.

Contents:

• Design a CRISPR/Cas experiment with gRNA and HiPlex panels (potato)
  • Create the reference sequences
  • Identify gRNAs
  • Create pairs of amplicons and gRNAs for all genes
  • Create pairs of amplicons and gRNAs for a subset of genes
• Design a CRISPR/Cas experiment with gRNA and HiPlex panels (microalgae)
  • Create the reference sequences
• Genetic diversity and composition analysis for wild and cultivated Coffea canephora
  • Characterization of the population structure and establishment of a core collection of wild C. canephora using GBS SNP markers
  • Characterization of the genetic composition and establishment of a core collection of cultivated C. canephora using HiPlex SNP markers
  • Core collection
• Population genetics of bullfrog, an invasive species
  • GBprocesS
  • Mapping reads with BWA-MEM
  • SMAP delineate
  • Effect of library size on genetic relationship estimations
  • Selection of good quality samples
  • Identify SNPs
  • SMAP haplotype-sites
  • SMAP relatedness