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Medientyp:
E-Artikel
Titel:
Fast construction of FM-index for long sequence reads
Beteiligte:
Li, Heng
Erschienen:
Oxford University Press (OUP), 2014
Erschienen in:Bioinformatics
Sprache:
Englisch
DOI:
10.1093/bioinformatics/btu541
ISSN:
1367-4811;
1367-4803
Entstehung:
Anmerkungen:
Beschreibung:
<jats:title>Abstract</jats:title>
<jats:p>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.</jats:p>
<jats:p>Availability and implementation: https://github.com/lh3/ropebwt2</jats:p>
<jats:p>Contact: hengli@broadinstitute.org</jats:p>