Scientific Publications

Fast construction of FM-index for long sequence reads.

Publication TypeJournal Article
AuthorsLi, H.
AbstractWe 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.
Year of Publication2014
JournalBioinformatics (Oxford, England)
Date Published (YYYY/MM/DD)2014/08/08
ISSN Number1367-4803
DOI10.1093/bioinformatics/btu541
PubMedhttp://www.ncbi.nlm.nih.gov/pubmed/25107872?dopt=Abstract