You are here

Bioinformatics DOI:10.1093/bioinformatics/btu541

Fast construction of FM-index for long sequence reads.

Publication TypeJournal Article
Year of Publication2014
AuthorsLi, H
JournalBioinformatics
Volume30
Issue22
Pages3274-5
Date Published2014 Nov 15
ISSN1367-4811
KeywordsAlgorithms, Genomics, Sequence Analysis, DNA
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: 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

Alternate JournalBioinformatics
PubMed ID25107872
PubMed Central IDPMC4221129
Grant ListGM100233 / GM / NIGMS NIH HHS / United States
U54HG003037 / HG / NHGRI NIH HHS / United States