Introduction

We present 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. We demonstrate its use on RNA-seq data and show that eXpress achieves greater efficiency than other quantification methods.

Publications

  1. Streaming fragment assignment for real-time analysis of sequencing experiments.
    Cite this
    Roberts A, Pachter L, 2013-01-01 - Nature methods

Credits

  1. Adam Roberts
    Developer

    Department of Computer Science, University of California, United States of America

  2. Lior Pachter
    Investigator

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT000386
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByLior Pachter