title: 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.
authors.affiliation: Department of Computer Science, University of California, Berkeley, Berkeley, California, USA.
authors.forename: Adam
authors.initials: A
authors.lastname: Roberts
authors.forename: Lior
authors.initials: L
authors.lastname: Pachter
mesh_terms: D000465:Algorithms; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology; D020869:Gene Expression Profiling / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D012313:RNA / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012313:RNA