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. 2022 Sep 15;38(18):4423-4425.
doi: 10.1093/bioinformatics/btac528.

The K-mer File Format: a standardized and compact disk representation of sets of k-mers

Yoann Dufresne  1 , Teo Lemane  2 , Pierre Marijon  3 , Pierre Peterlongo  2 , Amatur Rahman  4 , Marek Kokot  5 , Paul Medvedev  4   6   7 , Sebastian Deorowicz  5 , Rayan Chikhi  1
Affiliations

The K-mer File Format: a standardized and compact disk representation of sets of k-mers

Yoann Dufresne et al. Bioinformatics. .

Abstract

Summary: Bioinformatics applications increasingly rely on ad hoc disk storage of k-mer sets, e.g. for de Bruijn graphs or alignment indexes. Here, we introduce the K-mer File Format as a general lossless framework for storing and manipulating k-mer sets, realizing space savings of 3-5× compared to other formats, and bringing interoperability across tools.

Availability and implementation: Format specification, C++/Rust API, tools: https://github.com/Kmer-File-Format/.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
Structure of the K-mer File Format with k = 10 and minimizers of size 8. Top right part: a toy k-mer set shown in plain text. Left part: The same k-mer set is represented in KFF. The top-left box is the file header and each following boxes are different sections. Bottom right part: alternatively, a Sequences section can be represented more succinctly by a Minimizer section which contains the same set of k-mers. For example, the first entry in the M section has sequence ACTG with its minimizer at position 3, hence it corresponds to sequence ACTAAACTGATG of size 12 (which is identical to the first entry in the R section), from which three k-mers can be extracted
See this image and copyright information in PMC

References

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