Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time

Schmidt, S.; Alanko, J. N.

doi:10.1101/2022.05.17.492399

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bioRxiv · 10.1101/2022.05.17.492399

Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time

Schmidt, S.·Alanko, J. N.

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Abstract

A fundamental operation in computational genomics is to reduce the input sequences to their constituent k-mers. For maximum performance of downstream applications it is important to store the k-mers in small space, while keeping the representation easy and efficient to use (i.e. without k-mer repetitions and in plain text). Recently, heuristics were presented to compute a near-minimum such representation. We present an algorithm to compute a minimum representation in optimal (linear) time and use it to evaluate the existing heuristics. For that, we present a formalisation of arc-centric bidirected de Bruijn graphs and carefully prove that it accurately models the k-mer spectrum of the input. Our algorithm first constructs the de Bruijn graph in linear time in the length of the input strings (for a fixed-size alphabet). Then it uses a Eulerian-cycle-based algorithm to compute the minimum representation, in time linear in the size of the output. 2012 ACM Subject ClassificationApplied computing [->] Computational biology; Theory of computation [->] Data compression; Theory of computation [->] Graph algorithms analysis; Theory of computation [->] Data structures design and analysis

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Schmidt, S., Alanko, J. N.. 2022-05-19. Eulertigs: minimum plain text representation of k-mer sets without repetitions in linear time. https://doi.org/10.1101/2022.05.17.492399

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