subread
The Subread software package is a tool kit for processing next-gen sequencing data. It includes Subread aligner, Subjunc exon-exon junction detector and featureCounts read summarization program.
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Download Latest Version (.zip)- SubreadUsersGuide.pdf
- SubreadUsersGuide.tex
- longread-mapping.c
- LRMbase-index.c
- LRMbase-index.h
- LRMchro-event.c
- LRMchro-event.h
- LRMconfig.h
- LRMfile-io.c
- LRMfile-io.h
- LRMhashtable.c
- LRMhashtable.h
- LRMhelper.c
- LRMhelper.h
- LRMseek-zlib.c
- LRMseek-zlib.h
- LRMsorted-hashtable.c
- LRMsorted-hashtable.h
- Makefile
- aligner.c
- build-sam-index.c
- cell-counts.c
- core-bigtable.c
- core-bigtable.h
- core-indel.c
- core-indel.h
- core-interface-aligner.c
- core-interface-subjunc.c
- core-junction.c
- core-junction.h
- core.c
- core.h
- coverage_calc.c
- del4-mmap-test.c
- detection-calls.c
- exon-algorithms.c
- exon-algorithms.h
- exon-align-indel.c
- exon-align.c
- filterJunctionTable.c
- flattenAnnotations.c
- fullscan.c
- fusion-align.c
- gen_long_chromosomes.c
- gen_rand_reads.c
- gene-algorithms.c
- gene-algorithms.h
- gene-value-index.c
- gene-value-index.h
- global-reassembly.c
- hashtable.c
- hashtable.h
- HelperFunctions.c
- HelperFunctions.h
- index-builder.c
- input-blc.c
- input-blc.h
- input-files.c
- input-files.h
- interval_merge.c
- interval_merge.h
- long-hashtable.c
- long-hashtable.h
- Makefile
- Makefile.FreeBSD
- Makefile.Linux
- Makefile.MacOS
- makefile.version
- Makefile.Windows
- mergeVCF.c
- propmapped.c
- qualityScores.c
- read-repair.c
- readSummary.c
- removeDupReads.c
- removeDupReads.h
- sam2fq.c
- sambam-file.c
- sambam-file.h
- samMappedBases.c
- seek-zlib.c
- seek-zlib.h
- SNPCalling.c
- SNPCalling.h
- sorted-hashtable.c
- sorted-hashtable.h
- subfilter.c
- SUBindel.c
- sublog.c
- sublog.h
- subread.h
- subtools.c
- test-fisher.c
- test-seek-zlib.c
- test_qs.c
- tx-unique.c
- tx-unique.h
- zlib_test.c
- test-in.BAM
- exactSNP-test.sh
- across_genes.gtf
- across_genes_r1.bam
- across_genes_r1.bam.ora
- across_genes_r1.sam
- across_genes_r1.sam.ora
- across_genes_r2.bam
- across_genes_r2.bam.ora
- across_genes_r2.sam
- across_genes_r2.sam.ora
- across_intron.gtf
- across_intron_r1.bam
- across_intron_r1.bam.ora
- across_intron_r1.sam
- across_intron_r1.sam.ora
- across_intron_r2.bam
- across_intron_r2.bam.ora
- across_intron_r2.sam
- across_intron_r2.sam.ora
- compare.sh
- corner-BINS.SAF
- corner-BINS.sam
- corner-BothEnds.ora
- corner-Chimeric.ora
- corner-DoNotSort.ora
- corner-EXON-ONLY.ora
- corner-Extend3.ora
- corner-Extend5.ora
- corner-Fraction.ora
- corner-fractions.ora
- corner-fractions.SAF
- corner-fractions.sam
- corner-IgnoreDup.ora
- corner-INDEL.ora
- corner-INDEL.sam
- corner-Jcounts-FA.ora
- corner-Jcounts-FA.ora.jcounts
- corner-Jcounts.ora
- corner-Jcounts.ora.jcounts
- corner-JUNC-ONLY.ora
- corner-JUNC.ora
- corner-JUNC.sam
- corner-LargestOverlap.ora
- corner-MaxOPs.ora
- corner-MinMAPQ.ora
- corner-MinOverlap.ora
- corner-MultiMapping.ora
- corner-NH-PM.ora
- corner-NH.ora
- corner-NH.sam
- corner-ONEEND-BOTH.ora
- corner-ONEEND.ora
- corner-ONEEND.sam
- corner-PEdist.ora
- corner-Read2Pos3.ora
- corner-Read2Pos5.ora
- corner-reduction.sam
- intron_between.bam
- intron_between.bam.ora
- intron_between.gtf
- intron_between.sam
- intron_between.sam.ora
- intron_between_nointron.bam
- intron_between_nointron.bam.ora
- intron_between_nointron.sam
- intron_between_nointron.sam.ora
- test-chralias.GTF
- test-chralias.ora
- test-chralias.SAF
- test-chralias.sam
- test-chralias.txt
- test-chrname.ora
- test-chrname.SAF
- test-chrname.sam
- test-dup.sam
- test-fracOverlap.ora
- test-fracOverlap.sam
- test-junc.sam
- test-minimum-35ext.ora
- test-minimum-3ext.ora
- test-minimum-5ext.ora
- test-minimum-5reduce.ora
- test-minimum-dup.ora
- test-minimum-FL.ora
- test-minimum-O.ora
- test-minimum-PE.ora
- test-minimum-SE.ora
- test-minimum-STR.ora
- test-minimum-UNSTR.ora
- test-minimum.bam
- test-minimum.GTF
- test-minimum.ora
- test-minimum.SAF
- test-minimum.sam
- featureCounts-test.sh
- test_chr_aliases.sh
- test_chr_inference.sh
- test_commonusage.sh
- test_corner_cases.sh
- test_featurelevel.sh
- test_minimal_example.sh
- junction-reads-A.fq
- junction-reads-B.fq
- subjunc-test.sh
- cigar-test-1.fq
- cigar-test-2.fq
- indel-test1.fq
- indel-test2.fq
- subfusion_test.fa
- subfusion_test2.fa
- test-err-mut-r1.fq.gz
- test-err-mut-r2.fq.gz
- test-error-r1.fq
- test-error-r2.fq
- test-noerror-r1.fq
- test-noerror-r2.fq
- readname_cigar_match.py
- readname_ora_match.py
- subread-align-test.sh
- chr901.fa
- test_all.sh
- Aligning.md
- README.md
// repository documentation
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