The paper introduces eXpress, a software package designed for efficient probabilistic assignment of ambiguously mapped sequenced fragments in real-time analysis of sequencing experiments. eXpress uses a streaming algorithm with linear run time and constant memory usage, making it suitable for large-scale sequencing data such as ChIP-seq, metagenomics, and RNA-seq. The authors address the computational challenges of fragment assignment, particularly in high-throughput sequencing experiments, by developing an online Expectation-Maximization (EM) algorithm that processes data one fragment at a time. This approach allows for dynamic parameter updates and efficient convergence, leading to improved accuracy and speed compared to traditional batch methods. eXpress is implemented in open-source software and is available for download, offering a significant advancement in the analysis of deep sequencing experiments. The paper also includes simulations and comparisons with other tools like RSEM and Cufflinks to demonstrate eXpress's superior performance in terms of speed, memory usage, and accuracy.The paper introduces eXpress, a software package designed for efficient probabilistic assignment of ambiguously mapped sequenced fragments in real-time analysis of sequencing experiments. eXpress uses a streaming algorithm with linear run time and constant memory usage, making it suitable for large-scale sequencing data such as ChIP-seq, metagenomics, and RNA-seq. The authors address the computational challenges of fragment assignment, particularly in high-throughput sequencing experiments, by developing an online Expectation-Maximization (EM) algorithm that processes data one fragment at a time. This approach allows for dynamic parameter updates and efficient convergence, leading to improved accuracy and speed compared to traditional batch methods. eXpress is implemented in open-source software and is available for download, offering a significant advancement in the analysis of deep sequencing experiments. The paper also includes simulations and comparisons with other tools like RSEM and Cufflinks to demonstrate eXpress's superior performance in terms of speed, memory usage, and accuracy.