Subread

Subread package: high-performance read alignment, quantification and mutation discovery.
The Subread package comprises a suite of software programs for processing next-gen sequencing read data including:

• Subread: a general-purpose read aligner which can align both genomic DNA-seq and RNA-seq reads. It can also be used to discover genomic mutations including short indels and structural variants.
• Subjunc: a read aligner developed for aligning RNA-seq reads and for the detection of exon-exon junctions. Gene fusion events can be detected as well.
• featureCounts: a software program developed for counting reads to genomic features such as genes, exons, promoters and genomic bins.
• Sublong: a long-read aligner that is designed based on seed-and-vote.
• exactSNP: a SNP caller that discovers SNPs by testing signals against local background noises.