Streaming Fragment Assignment for Real-time Analysis of Sequencing Experiments

Overview

Journal Nat Methods

Specialties Biomedical Engineering
Pathology

Date 2012 Nov 20

PMID 23160280

Citations 514

Authors

Adam Roberts

Lior Pachter

Affiliations

Soon will be listed here.

Abstract

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.

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