SCExecute generates cell-barcode specific BAM files from aligned, aggregate single-cell sequencing data, executing a user-provided command on each barcode-stratified BAM file.

SCReadCounts is a computational tool for a cell-level assessment of the read counts bearing a particular nucleotide at genomic positions of interest from single cell RNA sequencing (scRNA-seq) data.

ReadCounts tabulates the number of reads providing evidence for variant and reference nucleotides at specific genomic loci and applies statistical tests to recognize allelic read-counts consistent with homozygous and heterozygous loci.

RNA2DNAlign evaluates evidence for asymmetric allele distribution in next-gen sequencing reads of DNA and RNA samples from the same individual.

SNPlice finds and evaluates the co-occurrence of single-nucleotide-polymorphisms (SNP) and altered splicing in next-gen mRNA sequence reads.