Tutorial

To further demonstrate the functionality of Parsnp we have prepared two small tutorial datasets. The first dataset is a MERS coronavirus outbreak dataset involving 42 isolates. The second dataset is a selected set of 31 Streptococcus pneumoniae genomes. Both of these datasets should run on modestly equipped laptops in a few minutes.

1. 42 MERS Coronavirus genomes

   • Download genomes:

     • gzipped tarball

   • Run parsnp

     ./parsnp -r ./mers42/England-Qatar_2012.fna -d ./mers42
     

   • Command-line output

   
   • Visualize with Gingr:
   

   • Inspect Output:

     • Multiple alignment: XMFA
     • SNPs: VCF
     • Phylogeny: Newick

2. 31 Streptococcus pneumoniae genomes

   • Download genomes:

     • gzipped tarball

   • Run parsnp

     ./parsnp -r ./strep31/NC_011900.fna -d ./strep31 -p <num threads>
     

   • Example output:

     

   • Force inclusion of all genomes (-c)

     ./parsnp -r ./strep31/NC_011900.fna -d ./strep31 -p <num threads> -c
     

• Command-line output:

  

• Visualize with Gingr

  

• Enable recombination detection/filter (-x)

  ./parsnp -r ./strep31/NC_011900.fna -d ./strep31 -p <num threads> -c -x
  

• Re-visualize with Gingr

  • Bootstrap values have improved after running recombination filter; columns with filtered SNPs are displayed in image: