Satsuma

Introduction

Synteny-focused aligner

Usage

To load the module:

module load satsuma

The main executable is

Satsuma

Help file output

Satsuma: Wrapper around high-sensitivity alignments.

Available arguments:

-q<string> : query fasta sequence
-t<string> : target fasta sequence
-o<string> : output directory
-l<int> : minimum alignment length (def=0)
-t_chunk<int> : target chunk size (def=4096)
-q_chunk<int> : query chunk size (def=4096)
-n<int> : number of blocks (def=1)
-lsf<bool> : submit jobs to LSF (def=0)
-nosubmit<bool> : do not run jobs (def=0)
-nowait<bool> : do not wait for jobs (def=0)
-chain_only<bool> : only chain the matches (def=0)
-refine_only<bool> : only refine the matches (def=0)
-min_prob<double> : minimum probability to keep match (def=0.99999)
-proteins<bool> : align in protein space (def=0)
-cutoff<double> : signal cutoff (def=1.8)
-same_only<bool> : only align sequences that have the same name. (def=0)
-self<bool> : ignore self-matches. (def=0)

Executables and scripts

The whole satsuma package involves the following executables:

BlockDisplaySatsuma  ChromosomePaintDensity  HomologyByXCorr          MicroSyntenyPlot      PapayaSeed         samples         SatsumaSynteny       SplitSatsuma
ChainMatches         ChromosomePaintNs       HomologyByXCorrSlave     MultiAlignCola        ReverseSatsumaOut  Satsuma         SatsumaSyntenyLight  test
checkLock            ColaAlignSatsuma        MakeDepend               OrderOrientBySynteny  runCola            SatsumaPop      SatsumaToFasta       test_Satsuma
Chromosemble         FilterGridSeeds         MergeScaffoldsBySynteny  OrientTranscripts     runPapaya          SatsumaStruct   ScaffoldBySynteny    test_SatsumaSynteny
ChromosomePaint      findColaSigDist         MergeXCorrMatches        PapayaDetails         runPapayaCola      SatsumaSummary  SortSatsuma          TestSComm