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

TL;DR

featureCounts is a fast, memory-efficient program for counting sequencing reads aligned to genomic features, significantly improving speed over existing methods and supporting various sequencing applications.

Contribution

It introduces a novel, highly efficient read summarization tool that outperforms existing methods in speed and memory usage for genomic feature counting.

Findings

Achieves an order of magnitude faster performance than previous tools

Uses less computer memory during read summarization

Supports both single and paired-end sequencing reads

Abstract

Next-generation sequencing technologies generate millions of short sequence reads, which are usually aligned to a reference genome. In many applications, the key information required for downstream analysis is the number of reads mapping to each genomic feature, for example to each exon or each gene. The process of counting reads is called read summarization. Read summarization is required for a great variety of genomic analyses but has so far received relatively little attention in the literature. We present featureCounts, a read summarization program suitable for counting reads generated from either RNA or genomic DNA sequencing experiments. featureCounts implements highly efficient chromosome hashing and feature blocking techniques. It is considerably faster than existing methods (by an order of magnitude for gene-level summarization) and requires far less computer memory. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications. featureCounts is available under GNU General Public License as part of the Subread (http://subread.sourceforge.net) or Rsubread (http://www.bioconductor.org) software packages.