GitHub - earonesty/STAR: RNA-seq aligner, ENCODE release

Name		Name	Last commit message	Last commit date
Mac_Include		Mac_Include
samtools		samtools
BAMfunctions.cpp		BAMfunctions.cpp
BAMfunctions.h		BAMfunctions.h
CHANGES		CHANGES
ErrorWarning.cpp		ErrorWarning.cpp
ErrorWarning.h		ErrorWarning.h
Genome.cpp		Genome.cpp
Genome.h		Genome.h
GlobalVariables.cpp		GlobalVariables.cpp
GlobalVariables.h		GlobalVariables.h
InOutStreams.cpp		InOutStreams.cpp
InOutStreams.h		InOutStreams.h
IncludeDefine.h		IncludeDefine.h
LICENSE		LICENSE
Makefile		Makefile
OutSJ.cpp		OutSJ.cpp
OutSJ.h		OutSJ.h
PackedArray.cpp		PackedArray.cpp
PackedArray.h		PackedArray.h
ParameterInfo.h		ParameterInfo.h
Parameters.cpp		Parameters.cpp
Parameters.h		Parameters.h
README		README
README_ENCODE		README_ENCODE
ReadAlign.cpp		ReadAlign.cpp
ReadAlign.h		ReadAlign.h
ReadAlignChunk.cpp		ReadAlignChunk.cpp
ReadAlignChunk.h		ReadAlignChunk.h
ReadAlignChunk_mapChunk.cpp		ReadAlignChunk_mapChunk.cpp
ReadAlignChunk_processChunks.cpp		ReadAlignChunk_processChunks.cpp
ReadAlign_assignAlignToWindow.cpp		ReadAlign_assignAlignToWindow.cpp
ReadAlign_createExtendWindowsWithAlign.cpp		ReadAlign_createExtendWindowsWithAlign.cpp
ReadAlign_mapOneRead.cpp		ReadAlign_mapOneRead.cpp
ReadAlign_maxMappableLength2strands.cpp		ReadAlign_maxMappableLength2strands.cpp
ReadAlign_multMapSelect.cpp		ReadAlign_multMapSelect.cpp
ReadAlign_oneRead.cpp		ReadAlign_oneRead.cpp
ReadAlign_outputAlignments.cpp		ReadAlign_outputAlignments.cpp
ReadAlign_outputTranscriptBAM.cpp		ReadAlign_outputTranscriptBAM.cpp
ReadAlign_outputTranscriptCIGARp.cpp		ReadAlign_outputTranscriptCIGARp.cpp
ReadAlign_outputTranscriptSAM.cpp		ReadAlign_outputTranscriptSAM.cpp
ReadAlign_outputTranscriptSJ.cpp		ReadAlign_outputTranscriptSJ.cpp
ReadAlign_stitchPieces.cpp		ReadAlign_stitchPieces.cpp
ReadAlign_stitchWindowSeeds.cpp		ReadAlign_stitchWindowSeeds.cpp
ReadAlign_storeAligns.cpp		ReadAlign_storeAligns.cpp
STAR		STAR
STAR.cpp		STAR.cpp
STARstatic		STARstatic
SequenceFuns.cpp		SequenceFuns.cpp
SequenceFuns.h		SequenceFuns.h
SjdbClass.h		SjdbClass.h
Stats.cpp		Stats.cpp
Stats.h		Stats.h
SuffixArrayFuns.cpp		SuffixArrayFuns.cpp
SuffixArraysFuns.h		SuffixArraysFuns.h
ThreadControl.cpp		ThreadControl.cpp
ThreadControl.h		ThreadControl.h
TimeFunctions.cpp		TimeFunctions.cpp
TimeFunctions.h		TimeFunctions.h
Transcript.cpp		Transcript.cpp
Transcript.h		Transcript.h
alignSmithWaterman.cpp		alignSmithWaterman.cpp
alignSmithWaterman.h		alignSmithWaterman.h
binarySearch2.cpp		binarySearch2.cpp
binarySearch2.h		binarySearch2.h
blocksOverlap.cpp		blocksOverlap.cpp
blocksOverlap.h		blocksOverlap.h
commentsENCODElong.txt		commentsENCODElong.txt
extendAlign.cpp		extendAlign.cpp
extendAlign.h		extendAlign.h
genomeGenerate.cpp		genomeGenerate.cpp
genomeGenerate.h		genomeGenerate.h
loadGTF.cpp		loadGTF.cpp
loadGTF.h		loadGTF.h
outputSJ.cpp		outputSJ.cpp
outputSJ.h		outputSJ.h
parametersDefault		parametersDefault
parametersDefault.xxd		parametersDefault.xxd
parametersENCODElong.txt		parametersENCODElong.txt
readLoad.cpp		readLoad.cpp
readLoad.h		readLoad.h
serviceFuns.cpp		serviceFuns.cpp
sjSplitAlign.cpp		sjSplitAlign.cpp
stitchAlignToTranscript.cpp		stitchAlignToTranscript.cpp
stitchAlignToTranscript.h		stitchAlignToTranscript.h
stitchGapIndel.cpp		stitchGapIndel.cpp
stitchWindowAligns.cpp		stitchWindowAligns.cpp
stitchWindowAligns.h		stitchWindowAligns.h
streamFuns.cpp		streamFuns.cpp
streamFuns.h		streamFuns.h
stringSubstituteAll.cpp		stringSubstituteAll.cpp
stringSubstituteAll.h		stringSubstituteAll.h
sysRemoveDir.cpp		sysRemoveDir.cpp
sysRemoveDir.h		sysRemoveDir.h

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STAR 2.3.1
Spliced Transcripts Alignment to a Reference
(c) Alexander Dobin, 2009-2014

AUTHOR/SUPPORT
Alex Dobin, dobin@cshl.edu
http://code.google.com/p/rna-star/
https://groups.google.com/d/forum/rna-star

INSTALLATION
To compile, unzip into a directory, and run 
$ make
Standard gnu c++ installation is required, with all the paths to libraries and include files supplied.
For Mac OS X run
$ make STARforMac


HARDWARE/SOFTWARE REQUIREMENTS 
x86-64 compatible processors
64 bit Linux or Mac OS X 
27GB of RAM for human genome 


LIMITATIONS:
----- This release was tested with the default parameters for human and mouse genomes.
Please contact the author for a list of recommended parameters for much larger or much smaller genomes.