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.

WWW: http://bioinf.wehi.edu.au/subread-package/