Fast construction of FM-index for long sequence reads.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 25107872.
- Also identified by DOI 10.1093/bioinformatics/btu541 and PMC identifier 4221129.
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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. https://github.com/lh3/ropebwt2 CONTACT: hengli@broadinstitute.org.
Medical subject headings
- Algorithms
- Sequence Analysis, DNA