# Fast construction of FM-index for long sequence reads

arXiv: https://arxiv.org/abs/1406.0426 · HTML: https://mlsanity.com/paper/1406.0426/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 2 Jun 2014.

## Built on by (most cited first, 1 of 1)

- [Infini-gram mini: Exact n-gram Search at the Internet Scale with FM-Index](https://mlsanity.com/paper/2506.12229/) (2025)

## Abstract (arXiv)

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