Fast construction of FM-index for long sequence reads
  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 
Heng Li
q-bio.GN cs.DS