Satsuma2¶
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.
Usage¶
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:
#!/bin/bash
#$ -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}