Fast construction of FM-index for long sequence reads

Heng Li

doi:10.1093/bioinformatics/btu541

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arXiv · 1406.0426

Fast construction of FM-index for long sequence reads

Heng Li

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Abstract

Summary: We present a new method to incrementally construct the FM-index for both short and long sequence reads, up to the size of a genome. It is the first algorithm that can build the index while implicitly sorting the sequences in the reverse (complement) lexicographical order without a separate sorting step. The implementation is among the fastest for indexing short reads and the only one that practically works for reads of averaged kilobases in length. Availability and implementation: https://github.com/lh3/ropebwt2 Contact: hengli@broadinstitute.org

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Heng Li. 2014-06-02. Fast construction of FM-index for long sequence reads. https://doi.org/10.1093/bioinformatics%2Fbtu541

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