ArticleBMC bioinformatics2021
MQF and buffered MQF: quotient filters for efficient storage of k-mers with their counts and metadata.
Article in BMC bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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Who cites it
1 citing paper in PubMed.
- Space-efficient representation of genomic k-mer count tables.Algorithms for molecular biology : AMB · 2022Article
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3 authors.
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Abstract
backgroundSpecialized data structures are required for online algorithms to efficiently handle large sequencing datasets. The counting quotient filter (CQF), a compact hashtable, can efficiently store k-mers with a skewed distribution.
resultHere, we present the mixed-counters quotient filter (MQF) as a new variant of the CQF with novel counting and labeling systems. The new counting system adapts to a wider range of data distributions for increased space efficiency and is faster than the CQF for insertions and queries in most of the tested scenarios. A buffered version of the MQF can offload storage to disk, trading speed of insertions and queries for a significant memory reduction. The labeling system provides a flexible framework for assigning labels to member items while maintaining good data locality and a concise memory representation. These labels serve as a minimal perfect hash function but are ~ tenfold faster than BBhash, with no need to re-analyze the original data for further insertions or deletions.
conclusionsThe MQF is a flexible and efficient data structure that extends our ability to work with high throughput sequencing data.
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