Streaming fragment assignment for real-time analysis of sequencing experiments.
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ABSTRACT:
SUBMITTER: Roberts A
PROVIDER: S-EPMC3880119 | biostudies-literature | 2013 Jan
REPOSITORIES: biostudies-literature
Publications
Streaming fragment assignment for real-time analysis of sequencing experiments.
Nature methods 20121118 1
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. ...[more]
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