Streaming fragment assignment for real-time analysis of sequencing experiments

A Roberts, L Pachter - Nature methods, 2013 - nature.com
Nature methods, 2013nature.com
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.
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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