6533b81ffe1ef96bd1277d8e
RESEARCH PRODUCT
Lightweight BWT Construction for Very Large String Collections
Markus J. BauerGiovanna RosoneAnthony J. Coxsubject
SequenceTheoretical computer scienceConstant (computer programming)BWTtext indexesComputer scienceString (computer science)Search engine indexingProcess (computing)Context (language use)next-generation sequencingAlphabetBWT; text indexes; next-generation sequencingdescription
A modern DNA sequencing machine can generate a billion or more sequence fragments in a matter of days. The many uses of the BWT in compression and indexing are well known, but the computational demands of creating the BWT of datasets this large have prevented its applications from being widely explored in this context. We address this obstacle by presenting two algorithms capable of computing the BWT of very large string collections. The algorithms are lightweight in that the first needs O(m log m) bits of memory to process m strings and the memory requirements of the second are constant with respect to m. We evaluate our algorithms on collections of up to 1 billion strings and compare their performance to other approaches on smaller datasets. Although our tests were on collections of DNA sequences of uniform length, the algorithms themselves apply to any string collection over any alphabet.
| year | journal | country | edition | language |
|---|---|---|---|---|
| 2011-01-01 |