Difference between revisions of "Satsuma"
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= Help file output = | = Help file output = | ||
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| + | Satsuma: Wrapper around high-sensitivity alignments. | ||
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| + | Available arguments: | ||
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-q<string> : query fasta sequence | -q<string> : query fasta sequence | ||
-t<string> : target fasta sequence | -t<string> : target fasta sequence | ||
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-same_only<bool> : only align sequences that have the same name. (def=0) | -same_only<bool> : only align sequences that have the same name. (def=0) | ||
-self<bool> : ignore self-matches. (def=0) | -self<bool> : ignore self-matches. (def=0) | ||
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| + | = Executables and scripts = | ||
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| + | The whole satsuma package involves the following executables: | ||
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| + | 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 | ||
Latest revision as of 14:04, 13 March 2017
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
