CircSeqAlignTk-package
                        CircSeqAlignTk: End-to-End Analysis of Small
                        RNA-Seq Data from Viroids
CircSeqAlignTkAlign-class
                        Class to store alignment results
CircSeqAlignTkCoverage-class
                        Class to save alignment coverage
CircSeqAlignTkRefIndex-class
                        Class to store reference information
CircSeqAlignTkSim-class
                        Class to save information of synthetic reads
align_reads             Align sequence reads to a genome sequence
build_app               Build a GUI application of CircSeqAlignTk
build_index             Build indexes of reference sequences for
                        alignment
calc_coverage           Calculate alignment coverage
filter_reads            Filter sequence reads in a FASTQ file by length
generate_reads          Generate synthetic sequence reads
merge.CircSeqAlignTkSim
                        Merge multiple synthetic datasets
plot_coverage           Visualize alignment coverage
