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Open Access Highly Accessed Methodology article

Improving read mapping using additional prefix grams

Jongik Kim1, Chen Li2 and Xiaohui Xie2*

Author Affiliations

1 Division of Computer Science & Engineering, Chonbuk National University, Jeonju, Republic of Korea

2 Department of Computer Science, University of California, Irvine, USA

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BMC Bioinformatics 2014, 15:42  doi:10.1186/1471-2105-15-42

Published: 5 February 2014



Next-generation sequencing (NGS) enables rapid production of billions of bases at a relatively low cost. Mapping reads from next-generation sequencers to a given reference genome is an important first step in many sequencing applications. Popular read mappers, such as Bowtie and BWA, are optimized to return top one or a few candidate locations of each read. However, identifying all mapping locations of each read, instead of just one or a few, is also important in some sequencing applications such as ChIP-seq for discovering binding sites in repeat regions, and RNA-seq for transcript abundance estimation.


Here we present Hobbes2, a software package designed for fast and accurate alignment of NGS reads and specialized in identifying all mapping locations of each read. Hobbes2 efficiently identifies all mapping locations of reads using a novel technique that utilizes additional prefix q-grams to improve filtering. We extensively compare Hobbes2 with state-of-the-art read mappers, and show that Hobbes2 can be an order of magnitude faster than other read mappers while consuming less memory space and achieving similar accuracy.


We propose Hobbes2 to improve the accuracy of read mapping, specialized in identifying all mapping locations of each read. Hobbes2 is implemented in C++, and the source code is freely available for download at webcite.

Next-generation sequencing; Read alignment; All mapper; Additional prefix q-gram; Hobbes2