This command will run minimap2 to find synteny between all maps of two genomes. 

create synteny <mapSetId1> <mapSetId2> [-p <minimap_parameters>]

The default parameters of minimap2 (-x asm5 -t 4 -m 1000) used by PersephoneShell set the limit on the minimal ribbon score (-m 1000). This threshold filters out a large number of secondary connectors and tries to leave only wide ribbons that show a "big picture":

The results of minimap2 are saved in a temporary *.paf file and stored in the database. The synteny ribbons are "anchored" to the track called "Synteny".

The default parameters can be changed by using the command line parameter -p (or --params):

create synteny 11 22 -p "-asm 5 -t 8 -m 10000"

Please watch the number of produced ribbons as it will affect the graphical performance of Persephone. We don't expect any issue if the synteny contains a few thousand of ribbons.

If minimap2 exits with an error, most likely it ran out of memory (Exit code:137). Try to reduce the number of threads (the parameter -t, which by default is set to 4).

The asm5 preset in minimap2 is designed for long assembly-to-reference mapping with sequence divergence below 5%. Here are the parameters equivalent to asm5:

  • -k19: K-mer size of 19
  • -w19: Minimizer window size of 19
  • -A1: Match score of 1
  • -B19: Mismatch penalty of 19
  • -O39,81: Gap open penalties of 39 (short gap) and 81 (long gap)
  • -E3,1: Gap extension penalties of 3 (short gap) and 1 (long gap)
  • -s200: Minimum chaining score of 200
  • -z200: Z-drop score of 200
  • -N50: Maximum number of chains per query of 50
  • --min-occ-floor=100: Minimum occurrence threshold of 100

These settings ensure that alignments do not extend into regions with 5% or higher sequence divergence. If your sequences have higher divergence, you might want to consider asm10 or asm20 presets instead.

Please consult the documentation for minimap2.