featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

Yang Liao, Gordon K. Smyth, Wei Shi

This paper describes featureCounts, a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoters, and genomic bins. The method implements highly efficient chromosome hashing and feature blocking techniques to achieve read counting speeds substantially faster than existing methods while maintaining accuracy.