Fast construction of FM-index for long sequence reads.
Bioinformatics
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| 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: CONTACT: hengli@broadinstitute.org. |
| Year of Publication | 2014
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| Journal | Bioinformatics
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| Volume | 30
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| Issue | 22
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| Pages | 3274-5
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| Date Published | 2014 Nov 15
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| ISSN | 1367-4811
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| URL | |
| DOI | 10.1093/bioinformatics/btu541
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| PubMed ID | 25107872
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| PubMed Central ID | PMC4221129
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| Grant list | GM100233 / GM / NIGMS NIH HHS / United States
U54HG003037 / HG / NHGRI NIH HHS / United States
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