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Bioinformatics (Oxford, England) DOI:10.1093/bioinformatics/btu541

Fast construction of FM-index for long sequence reads.

Publication TypeJournal Article
Year of Publication2014
AuthorsLi, H
JournalBioinformatics (Oxford, England)
Date Published2014/08/08
ISSN1367-4803
Abstract

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.

URLhttp://bioinformatics.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=25107872
DOI10.1093/bioinformatics/btu541
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/25107872?dopt=Abstract