eXpress – a tool for quantification of RNA-Seq data

Scientists at the University of California, Berkeley have developed eXpress, a software package for efficient probabilistic assignment of ambiguously mapping sequenced fragments. eXpress uses a streaming algorithm with linear run time and constant memory use. It can determine abundances of sequenced molecules in real time and can be applied to ChIP-seq, metagenomics and other large-scale sequencing data. They demonstrate its use on RNA-seq data and show that eXpress achieves greater efficiency than other quantification methods.

The eXpress software is freely available as Supplementary Software and at


  • Roberts A, Pachter L. (2012) Streaming fragment assignment for real-time analysis of sequencing experiments. Nat Methods [Epub ahead of print]. [abstract]
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