Ben Langmead

The paper introduces ms2, a suite of algorithms for efficiently computing matching statistics and SMEMs in compressed pangenome indexes, achieving significant speedups over existing methods.

SIFT selects reference haplotypes for genome patching using compressed indexing and pseudo-MEM queries to improve T2T imputation efficiency.

Ok-k-mer selects optimal k-mer length ensembles to improve genomic distance estimation by maximizing correlation with phylogenetic branch distances.

This paper introduces RGRs, genomic repeats that enable high-resolution single-cell molecular recording, validated in live mice for long-term gene activity tracking.

ImpuT2T patches gaps in HiFi assemblies using pangenomes, improving quality over existing methods.

Shredtools uses multi-MUMs to enable efficient querying of pangenome coordinates, allowing rapid extraction of gene regions across multiple genomes.

The paper introduces algorithms for constructing RLBWT-based compressed full text indexes in compressed space, reducing memory usage for large-scale pangenome analysis.

Movi 2 improves pangenome indexing by reducing memory footprint and enabling space-time tradeoffs for efficient querying.

This paper introduces a run-length compressed metagenomic read classification method that outperforms existing tools in accuracy and runtime while maintaining efficient memory usage.

This paper extends Chromap to provide peak-based quality control metrics for single-cell ATAC-seq without peak calling, improving downstream analysis by identifying low-quality cells missed by other methods.

The paper introduces a new open-source tool for efficient genomic sequence digestion using minimizers, modimizers, or syncmers.

Mumemto efficiently computes multi-MUMs across large pangenomes to visualize synteny and detect structural variations.

Movi Color improves long-read classification accuracy and speed using a move structure and color-based indexing, outperforming existing methods in precision and recall.

The paper extends the Mumemto tool to compute multi-MUMs across large pangenomes using new partitioning strategies, enabling scalability to 474 human haplotypes.

The paper benchmarks ANI estimation algorithms using simulated and real datasets, showing that ANIb is most accurate but least efficient, while k-mer approaches are efficient and accurate, with some clades requiring multiple k-values.

The paper improves pangenomic classification accuracy by introducing chain statistics that capture coarse-grained co-linearity without requiring chaining algorithms.

Movi is a fast pangenome index that enables efficient querying of nanopore sequencing reads using move structures, achieving faster speeds than existing methods.

IGLoo improves the analysis of immunoglobulin heavy chain locus assemblies in lymphoblastoid cell lines by characterizing somatic recombination events and enhancing germline assembly quality.

Sigmoni classifies nanopore signals using a compressed pangenome index, enabling efficient and accurate classification of reads against large references.

Cliffy improves 16S rRNA classification by reducing index size and increasing accuracy compared to Kraken2 and Bracken.

The paper introduces MEMO, a pangenome indexing method that efficiently handles k-mer queries and conservation analysis across pangenomes.

Centrifuger compresses microbial genomes losslessly for faster and more accurate metagenomic classification by reducing memory use and improving taxonomic resolution.

The paper introduces biastools to measure and diagnose reference bias in genomic data across different scenarios and finds that inclusive graph genomes and end-to-end alignment reduce bias.

DandD measures sequence growth and similarity in genome assemblies using a new metric called delta, estimating how much new sequence is added and when discoveries will plateau.

The paper introduces levioSAM2, a method for accurate lift-over between genome assemblies, improving variant calling accuracy when mapping to older references.

The paper introduces an impute-first alignment framework that improves variant calling accuracy and efficiency by using a personalized diploid reference.

The paper introduces Wheelie, an algorithm to check if a graph has Wheeler properties, and presents the WGT toolkit for visualizing and generating Wheeler graphs.

Dashing 2 improves genomic sketching by incorporating k-mer multiplicities and scaling all-pairs comparisons to millions of sequences using locality-sensitive hashing.

SPUMONI 2 improves pangenome classification by using a compressed index of minimizer digests, achieving faster speed, lower memory use, and better performance for short and long reads.

The paper introduces rowbowt, a tool for pangenomic genotyping using a marker array to improve accuracy and efficiency over existing methods.