Skip to content


Satsuma2 is an optimised version of Satsuma, a tool to reliably align large and complex DNA sequences.

Satsuma2 is available as a module on Apocrita.


To run the default installed version of Satsuma2, simply load the satsuma2 module:

$ module load satsuma2
Usage:   <command> [options]

The following commands are available:

BlockDisplaySatsuma     MatchesByFeature
ChainMatches            MergeScaffoldsBySynteny
Chromosemble            MergeXCorrMatches
ChromosomePaint         MicroSyntenyPlot
ColaAlignSatsuma        OrderOrientBySynteny
FilterGridSeeds         ReverseSatsumaOut
HomologyByXCorr         SatsumaSynteny2
HomologyByXCorrSlave    SatsumaToFASTA
KMatch                  SatsumaToGFF
MatchDump               SortSatsuma

Usage for each command can be shown by running the command without options.

Example job

Here is an example job running the SatsumaSynteny2 tool, using 2 cores and 4G of memory:

#$ -cwd
#$ -j y
#$ -pe smp 2
#$ -l h_rt=1:0:0
#$ -l h_vmem=2G

module load satsuma2

SatsumaSynteny2 \
  -q input1.fasta \
  -t input2.fasta \
  -o output-directory \
  -threads ${NSLOTS}