TrendBio

#36 · Tools & infrastructure

Index-free and compressed structures speed sequence search and alignment at scale

2 preprints · 1 published
Items per day, last 8 weekstoday: 3

The dominant thread across these items is engineering sequence search and alignment for throughput and memory efficiency at scale. IndelFreeAligner is a streaming, indel-free aligner that avoids reference pre-indexing and is benchmarked against Bowtie1 and BLAST+ on terabase-scale references. RSHash, a published method, is a compressed static k-mer hash built on rank-select bitvectors and layered minimizers, reported as about 40% faster than SSHash at equal memory. Reseek v3 is more accuracy-oriented, using parallel alignment over rich discrete structure alphabets with level-specific statistical models for protein structure search. What is new is the combination of index design, streaming execution, and alphabet choice, with the two sequence-level tools emphasizing speed and memory and Reseek v3 emphasizing accuracy.

Published papers

  • RSHash: a fast and space-efficient hash table for k-mers.

    Bioinformatics (Oxford, England)Jonas Schulte-Mattler et al.

    RSHash, a compressed static k-mer hash using rank-select bitvectors and layered minimizers, is about 40% faster than SSHash at equal memory, reaching 8 bits…

Preprints

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