Streaming fragment assignment for real-time analysis of sequencing experiments.

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.

SUBMITTER: Roberts A 

PROVIDER: S-EPMC3880119 | biostudies-literature | 2013 Jan

REPOSITORIES: biostudies-literature