STAR

(★ 2,236)

RNA-seq aligner

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Download Latest Version (.zip)

- - STAR
  - STARlong
- - STAR
  - STARlong
- - STAR
  - STARlong
- STARmanual.pdf
- STARconsensus.md
- STARsolo.md
- - convertParDefToLatexTable.awk
  - parametersDefault.tex
  - STARmanual.tex
- - Dockerfile
- - ENCODE.txt
- - calcInsertCoverage.awk
  - extractSJfromGTF.sh
  - filterCirc.awk
  - mergeGeneCounts.awk
  - mergeLogFinal.awk
  - mergeSuperContig.awk
  - sjBED12.awk
  - sjCollapseSamples.awk
  - sjFromSAMcollapseUandM.awk
  - sjFromSAMcollapseUandM_inclOverlaps.awk
  - sjMotif.m
  - soloBasicCellFilter.awk
  - soloCompareMtx.awk
  - soloCountMatrixFromBAM.awk
  - soloExtractFiltCells.awk
  - soloUMIperCell.awk
  - tagXSstrandedData.awk
  - transcriptTypes.awk
  - transfragsFromBedGraph.awk
- - .gitignore
  - .travis.yml
  - bgzf.c
  - bgzip.c
  - config.h
  - faidx.5
  - faidx.c
  - hfile.c
  - hfile_internal.h
  - hfile_net.c
  - hts.c
  - htslib.mk
  - htslib_vars.mk
  - kfunc.c
  - knetfile.c
  - kstring.c
  - Makefile
  - README.md
  - sam.5
  - sam.c
  - synced_bcf_reader.c
  - tabix.1
  - tabix.c
  - tbx.c
  - vcf.5
  - vcf.c
  - vcf_sweep.c
  - vcfutils.c
- - LICENSE
  - opal.cpp
  - opal.h
  - simde_avx2.h
- - ReadMe.txt
  - sgt.h
- AlignVsTranscript.h
- bam_cat.c
- bam_cat.h
- BAMbinSortByCoordinate.cpp
- BAMbinSortByCoordinate.h
- BAMbinSortUnmapped.cpp
- BAMbinSortUnmapped.h
- BAMfunctions.cpp
- BAMfunctions.h
- BAMoutput.cpp
- BAMoutput.h
- bamRemoveDuplicates.cpp
- bamRemoveDuplicates.h
- bamSortByCoordinate.cpp
- bamSortByCoordinate.h
- binarySearch2.cpp
- binarySearch2.h
- blocksOverlap.cpp
- blocksOverlap.h
- Chain.cpp
- Chain.h
- ChimericAlign.cpp
- ChimericAlign.h
- ChimericAlign_chimericBAMoutput.cpp
- ChimericAlign_chimericJunctionOutput.cpp
- ChimericAlign_chimericStitching.cpp
- ChimericDetection.cpp
- ChimericDetection.h
- ChimericDetection_chimericDetectionMult.cpp
- ChimericSegment.cpp
- ChimericSegment.h
- ChimericTranscript.h
- ClipCR4.cpp
- ClipCR4.h
- ClipMate.h
- ClipMate_clip.cpp
- ClipMate_clipChunk.cpp
- ClipMate_initialize.cpp
- ErrorWarning.cpp
- ErrorWarning.h
- extendAlign.cpp
- extendAlign.h
- funCompareUintAndSuffixes.cpp
- funCompareUintAndSuffixes.h
- funCompareUintAndSuffixesMemcmp.cpp
- funCompareUintAndSuffixesMemcmp.h
- funPrimaryAlignMark.cpp
- funPrimaryAlignMark.h
- Genome.cpp
- Genome.h
- Genome_genomeGenerate.cpp
- Genome_genomeLoad.cpp
- Genome_genomeOutLoad.cpp
- Genome_insertSequences.cpp
- Genome_transformGenome.cpp
- genomeGenerate.h
- genomeParametersWrite.cpp
- genomeParametersWrite.h
- genomeSAindex.cpp
- genomeSAindex.h
- genomeScanFastaFiles.cpp
- genomeScanFastaFiles.h
- GlobalVariables.cpp
- GlobalVariables.h
- GTF.cpp
- GTF.h
- GTF_superTranscript.cpp
- GTF_transcriptGeneSJ.cpp
- IncludeDefine.h
- InOutStreams.cpp
- InOutStreams.h
- insertSeqSA.cpp
- insertSeqSA.h
- Makefile
- mapThreadsSpawn.cpp
- mapThreadsSpawn.h
- outputSJ.cpp
- outputSJ.h
- OutSJ.cpp
- OutSJ.h
- PackedArray.cpp
- PackedArray.h
- ParameterInfo.h
- Parameters.cpp
- Parameters.h
- Parameters_closeReadsFiles.cpp
- Parameters_openReadsFiles.cpp
- Parameters_readFilesInit.cpp
- Parameters_readSAMheader.cpp
- Parameters_samAttributes.cpp
- ParametersChimeric.h
- ParametersChimeric_initialize.cpp
- ParametersClip.h
- ParametersClip_initialize.cpp
- parametersDefault
- ParametersGenome.cpp
- ParametersGenome.h
- ParametersSolo.cpp
- ParametersSolo.h
- Quantifications.cpp
- Quantifications.h
- ReadAlign.cpp
- ReadAlign.h
- ReadAlign_alignBAM.cpp
- ReadAlign_assignAlignToWindow.cpp
- ReadAlign_calcCIGAR.cpp
- ReadAlign_chimericDetection.cpp
- ReadAlign_chimericDetectionOld.cpp
- ReadAlign_chimericDetectionOldOutput.cpp
- ReadAlign_chimericDetectionPEmerged.cpp
- ReadAlign_CIGAR.cpp
- ReadAlign_createExtendWindowsWithAlign.cpp
- ReadAlign_mapOneRead.cpp
- ReadAlign_mapOneReadSpliceGraph.cpp
- ReadAlign_mappedFilter.cpp
- ReadAlign_maxMappableLength2strands.cpp
- ReadAlign_multMapSelect.cpp
- ReadAlign_oneRead.cpp
- ReadAlign_outputAlignments.cpp
- ReadAlign_outputSpliceGraphSAM.cpp
- ReadAlign_outputTranscriptCIGARp.cpp
- ReadAlign_outputTranscriptSAM.cpp
- ReadAlign_outputTranscriptSJ.cpp
- ReadAlign_outputVariation.cpp
- ReadAlign_peOverlapMergeMap.cpp
- ReadAlign_quantTranscriptome.cpp
- ReadAlign_stitchPieces.cpp
- ReadAlign_stitchWindowSeeds.cpp
- ReadAlign_storeAligns.cpp
- ReadAlign_transformGenome.cpp
- ReadAlign_waspMap.cpp
- ReadAlignChunk.cpp
- ReadAlignChunk.h
- ReadAlignChunk_mapChunk.cpp
- ReadAlignChunk_processChunks.cpp
- ReadAnnotations.h
- readBarcodeLoad.h
- readLoad.cpp
- readLoad.h
- samHeaders.cpp
- samHeaders.h
- SequenceFuns.cpp
- SequenceFuns.h
- serviceFuns.cpp
- SharedMemory.cpp
- SharedMemory.h
- signalFromBAM.cpp
- signalFromBAM.h
- sjAlignSplit.cpp
- sjAlignSplit.h
- sjdbBuildIndex.cpp
- sjdbBuildIndex.h
- SjdbClass.h
- sjdbInsertJunctions.cpp
- sjdbInsertJunctions.h
- sjdbLoadFromFiles.cpp
- sjdbLoadFromFiles.h
- sjdbLoadFromStream.cpp
- sjdbLoadFromStream.h
- sjdbPrepare.cpp
- sjdbPrepare.h
- Solo.cpp
- Solo.h
- SoloBarcode.cpp
- SoloBarcode.h
- SoloBarcode_extractBarcode.cpp
- SoloCommon.h
- SoloFeature.cpp
- SoloFeature.h
- SoloFeature_addBAMtags.cpp
- SoloFeature_cellFiltering.cpp
- SoloFeature_collapseUMI_Graph.cpp
- SoloFeature_collapseUMIall.cpp
- SoloFeature_countCBgeneUMI.cpp
- SoloFeature_countSmartSeq.cpp
- SoloFeature_countVelocyto.cpp
- SoloFeature_emptyDrops_CR.cpp
- SoloFeature_loadRawMatrix.cpp
- SoloFeature_outputResults.cpp
- SoloFeature_processRecords.cpp
- SoloFeature_quantTranscript.cpp
- SoloFeature_redistributeReadsByCB.cpp
- SoloFeature_statsOutput.cpp
- SoloFeature_sumThreads.cpp
- SoloFeatureTypes.h
- SoloFilteredCells.h
- soloInputFeatureUMI.cpp
- soloInputFeatureUMI.h
- SoloRead.cpp
- SoloRead.h
- SoloRead_record.cpp
- SoloReadBarcode.cpp
- SoloReadBarcode.h
- SoloReadBarcode_getCBandUMI.cpp
- SoloReadBarcodeStats.h
- SoloReadFeature.cpp
- SoloReadFeature.h
- SoloReadFeature_inputRecords.cpp
- SoloReadFeature_record.cpp
- SoloReadFeatureStats.h
- sortSuffixesBucket.h
- SpliceGraph.cpp
- SpliceGraph.h
- SpliceGraph_findSuperTr.cpp
- SpliceGraph_swScoreSpliced.cpp
- SpliceGraph_swTraceBack.cpp
- STAR.cpp
- Stats.cpp
- Stats.h
- stitchAlignToTranscript.cpp
- stitchAlignToTranscript.h
- stitchGapIndel.cpp
- stitchWindowAligns.cpp
- stitchWindowAligns.h
- streamFuns.cpp
- streamFuns.h
- stringSubstituteAll.cpp
- stringSubstituteAll.h
- SuffixArrayFuns.cpp
- SuffixArrayFuns.h
- SuperTranscriptome.cpp
- SuperTranscriptome.h
- sysRemoveDir.cpp
- sysRemoveDir.h
- systemFunctions.cpp
- systemFunctions.h
- Test.hpp
- ThreadControl.cpp
- ThreadControl.h
- TimeFunctions.cpp
- TimeFunctions.h
- Transcript.cpp
- Transcript.h
- Transcript_alignScore.cpp
- Transcript_convertGenomeCigar.cpp
- Transcript_generateCigarP.cpp
- Transcript_transformGenome.cpp
- Transcript_variationAdjust.cpp
- Transcript_variationOutput.cpp
- Transcriptome.cpp
- Transcriptome.h
- Transcriptome_alignExonOverlap.cpp
- Transcriptome_classifyAlign.cpp
- Transcriptome_geneCountsAddAlign.cpp
- Transcriptome_geneFullAlignOverlap.cpp
- Transcriptome_geneFullAlignOverlap_ExonOverIntron.cpp
- Transcriptome_quantAlign.cpp
- twoPassRunPass1.cpp
- twoPassRunPass1.h
- Variation.cpp
- Variation.h
- VERSION
.gitignore
.gitmodules
.travis.yml
_config.yml
CHANGES.md
CODE_OF_CONDUCT.md
CONTRIBUTING.md
LICENSE
README.md
RELEASEnotes.md

# Installation Guide

1. Get the code

git clone https://github.com/alexdobin/STAR

Downloads the entire project code from GitHub to your computer.

cd STAR

Moves into the project folder you just downloaded.

2. Docker

Easy Recommended

Prerequisites

Git Needed to download the project code from GitHub.
Docker Desktop Needed to build and run containers. Install it and keep it running in the background.

⚠️ This is a large repository, so this method may point to an internal sub-package rather than the actual core product. Check the full README as well.

docker build -f extras/docker/Dockerfile -t star .

Builds a runnable image based on the Dockerfile.

docker run -p 8080:80 star

Runs the built image as an actual container.

✅ Run docker compose ps to check the containers are Up. If the README mentions a port, open http://localhost:PORT in your browser.

3. Make

Medium

Prerequisites

Git Needed to download the project code from GitHub.
Make Usually pre-installed on Linux/macOS. On Windows, install separately (e.g. via MSYS2 or WSL).

make STAR