Turtle: Identifying frequent k-mers with cache-efficient algorithms

Counting the frequencies of k-mers in read libraries is often a first step in the analysis of high-throughput sequencing experiments. Infrequent k-mers are assumed to be a result of sequencing errors. The frequent k-mers constitute a reduced but error-free representation of the experiment, which can inform read error correction or serve as the input to de novo assembly methods. Ideally, the memory requirement for counting should be linear in the number of frequent k-mers and not in the, typically much larger, total number of k-mers in the read library.

We present a novel method that balances time, space and accuracy requirements to efficiently extract frequent k-mers even for high coverage libraries and large genomes such as human. Our method is designed to minimize cache-misses in a cache-efficient manner by using a Pattern-blocked Bloom filter to remove infrequent k-mers from consideration in combination with a novel sort-and-compact scheme, instead of a Hash, for the actual counting. While this increases theoretical complexity, the savings in cache misses reduce the empirical running times. A variant can resort to a counting Bloom filter for even larger savings in memory at the expense of false negatives in addition to the false positives common to all Bloom filter based approaches. A comparison to the state-of-the-art shows reduced memory requirements and running times.

The source can be downloaded from here.

The example read files can be downloaded from sample.fa. and sample.fq.

For further information contact Rajat S Roy (rajatroy@cs.rutgers.edu). This software is a result of or used in the following projects: SCG, HTSMethods, AlgoEngineering.


Members: Rajat S Roy, Alexander Schliep. Collaborators: Debashish Bhattacharya (Department of Ecology, Evolution, and Natural Resources, Rutgers).