Satsuma - Revision history

Rf at 14:04, 13 March 2017

2017-03-13T14:04:41Z

Rf at 14:11, 10 March 2017

2017-03-10T14:11:18Z

Rf: Created page with "= Introduction = Synteny-focused aligner = Usage = To load the module: module load satsuma The main executable is Satsuma = Help file output = Satsuma: Wrapper around..."

2017-03-10T14:10:57Z

Created page with "= Introduction = Synteny-focused aligner = Usage = To load the module: module load satsuma The main executable is Satsuma = Help file output = Satsuma: Wrapper around..."

New page

= 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)

← Older revision		Revision as of 14:04, 13 March 2017
Line 35:		Line 35:
	-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)
		+
		+	= 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

@@ Line 13: / Line 13: @@
 = Help file output =
   -q<string> : query fasta sequence
   -t<string> : target fasta sequence