TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files. The input parameters are the same GTF files used to generate the alignments, and one or multiple input BAM file(s) containing either single-end or paired-end sequencing reads. The TPMCalculator output is comprised of four files per sample reporting the TPM values and raw read counts for genes, transcripts, exons and introns respectively.

a fast, flexible C++ API & toolkit for reading, writing, and manipulating BAM files.

(Genome Analysis Toolkit) a software package developed to analyze high-throughput sequencing data capable of taking on projects of any size with a primary focus on variant discovery, genotyping, and data quality assurance.

TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files. The input parameters are the same GTF files used to generate the alignments, and one or multiple input BAM file(s) containing either single-end or paired-end sequencing reads. The TPMCalculator output is comprised of four files per sample reporting the TPM values and raw read counts for genes, transcripts, exons and introns respectively.

redistributable software libraries to support CUDA applications for Linux.

a Python distribution that includes more than 400 of the most popular Python packages for science, math, engineering, and data analysis.

Performs haplotype phasing using read alignments in BAM format from both DNA and RNA based assays, and provides measures of haplotypic expression for RNA based assays.