Matchtigs: minimum plain text representation of k-mer sets

Matchtigs: minimum plain text representation of k-mer sets

Abstract We propose a polynomial algorithm computing a minimum plain-text representation of k-mer sets, as well as an efficient near-minimum greedy heuristic. When compressing read sets of large model organisms or bacterial pangenomes, with only a minor runtime increase, we shrink the representation...

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Bibliographic Details
Main Authors: Sebastian Schmidt, Shahbaz Khan, Jarno N. Alanko, Giulio E. Pibiri, Alexandru I. Tomescu
Format: Article
Language:English
Published: BMC 2023-06-01
Series:Genome Biology
Subjects:
k-mer sets
Plain text compression
Graph algorithm
Sequence analysis
Genomic sequences
Minimum-cost flow
Online Access:https://doi.org/10.1186/s13059-023-02968-z

Internet

https://doi.org/10.1186/s13059-023-02968-z

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