strobemers

strobemers provide an alternative to k-mer-based sequence comparison by using linked minimizers to improve robustness to variable mutation rates and indels and to increase match distribution and coverage.

Key Features:

• Linked Minimizers: Strobemers consist of linked minimizers that maintain consistency across sequences despite mutations.
• Reduced Sensitivity to Mutation Rates: Strobemers reduce sensitivity to variable mutation rates compared to k-mer and spaced k-mer methods by preventing a single mutation from affecting consecutive strobemers.
• Improved Match Distribution: Simulated data show that strobemers yield more evenly distributed sequence matches across sequences.
• Higher Match Coverage: Strobemers achieve higher match coverage than k-mers, aiding comprehensive alignment and clustering of sequences.
• Handling Indels Effectively: Strobemers integrate indel handling into their matching strategy, reducing redundancy relative to methods that rely on k-mer matches followed by pairing or grouping.

Scientific Applications:

• Sequence Clustering: Strobemers facilitate accurate clustering by providing more evenly distributed sequence matches for grouping similar genetic material.
• Alignment Scenarios: The indel robustness and high match coverage of strobemers make them suitable for aligning sequences in diverse biological datasets.

Methodology:

Strobemers are generated and evaluated via a repository-based implementation; a proof-of-concept tool, StrobeMap, demonstrates their utility using synthetic and biological Oxford Nanopore sequencing data.