Counts NGS read alignments against GTF annotations in a multithreaded and scalable fashion.
Benchmark: 8 core 1M annotations for 2Gb sorted reads ~30 seconds compared to ~28 minutes for bedtools multicov.
Files include:
fast_count_multi - reports all counts and RPKM, multithreading support
fast_count_deseq - reports gene counts in deseq compatible format, multithreading support
fast_count - reports all counts with no multithreading support.
usage
./fast_count_multi num_threads...