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:

    • Run parsnp

      ./parsnp -r ./mers42/England-Qatar_2012.fna -d ./mers42
    • Command-line output

    • Visualize with Gingr:
    • Inspect Output:

  2. 31 Streptococcus pneumoniae genomes

    • Download genomes:

    • 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: