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Open Access Highly Accessed Methodology article

Fragment assignment in the cloud with eXpress-D

Adam Roberts1, Harvey Feng1 and Lior Pachter12*

Author Affiliations

1 Department of Computer Science, 387 Soda Hall, UC Berkeley, Berkeley, CA 94720, USA

2 Departments of Mathematics and Molecular & Cell Biology, 970 Evans Hall, UC Berkeley, Berkeley, CA 94720, USA

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BMC Bioinformatics 2013, 14:358  doi:10.1186/1471-2105-14-358

Published: 7 December 2013



Probabilistic assignment of ambiguously mapped fragments produced by high-throughput sequencing experiments has been demonstrated to greatly improve accuracy in the analysis of RNA-Seq and ChIP-Seq, and is an essential step in many other sequence census experiments. A maximum likelihood method using the expectation-maximization (EM) algorithm for optimization is commonly used to solve this problem. However, batch EM-based approaches do not scale well with the size of sequencing datasets, which have been increasing dramatically over the past few years. Thus, current approaches to fragment assignment rely on heuristics or approximations for tractability.


We present an implementation of a distributed EM solution to the fragment assignment problem using Spark, a data analytics framework that can scale by leveraging compute clusters within datacenters–“the cloud”. We demonstrate that our implementation easily scales to billions of sequenced fragments, while providing the exact maximum likelihood assignment of ambiguous fragments. The accuracy of the method is shown to be an improvement over the most widely used tools available and can be run in a constant amount of time when cluster resources are scaled linearly with the amount of input data.


The cloud offers one solution for the difficulties faced in the analysis of massive high-thoughput sequencing data, which continue to grow rapidly. Researchers in bioinformatics must follow developments in distributed systems–such as new frameworks like Spark–for ways to port existing methods to the cloud and help them scale to the datasets of the future. Our software, eXpress-D, is freely available at: webcite.