Fast construction of FM-index for long sequence reads

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: [email protected]

arXiv comment2 pages

References in corpus (2)

• Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform
• GPU-Accelerated BWT Construction for Large Collection of Short Reads

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