TutorialΒΆ
To further demonstrate the functionality of Parsnp we have prepared two small tutorial datasets. The first dataset is a MERS coronavirus outbreak dataset involving 49 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.
49 MERS Coronavirus genomes
Download genomes:
Run parsnp with default parameters
./parsnp -g ./ref/EMC_2012.gbk -d ./mers49 -cCommand-line output
- Visualize with Gingr GGR
Configure parameters
95% of the reference is covered by the alignment. This is <100% mainly due to a 1kbp unaligned region from 26kbp to 27kbp.
To force alignment across large collinear regions, use the -C maximum distance between two collinear MUMs:
./parsnp -g ./ref/EMC_2012.gbk -d ./mers49 -C 1000 -cVisualize again with Gingr GGR
Zoom in with Gingr for nucleotide view of region
Inspect Output:
31 Streptococcus pneumoniae genomes
Download genomes:
Run parsnp
./parsnp -r ./strep31/NC_011900.fna -d ./strep31 -p <num threads>Command-line output:
Force inclusion of all genomes (-c)
./parsnp -r ./strep31/NC_011900.fna -d ./strep31 -p <num threads> -c
Command-line output: