Guillaume Holley

The paper describes using kallisto, bustools, and kb-python to quantify RNA-seq data from bulk, single-cell, and single-nucleus samples.

This paper introduces a method to improve RNA-seq quantification by expanding the transcriptome reference to include both nascent and mature mRNA and using distinguishing flanking k-mers to enhance mapping accuracy.

The paper analyzes whole genome sequences of 150,119 UK Biobank individuals, identifying variants and associations with traits, and provides a haplotype reference panel for imputation.

PopIns2 detects non-reference sequence variants across large genome datasets using a colored de Bruijn graph approach, showing improved scalability and precision.

The paper uses long-read sequencing on 3,622 Icelanders to identify structural variants and their associations with diseases and traits.

BlastFrost efficiently queries bacterial genomes using Bifrost graphs to identify gene presence and SNVs in large collections.

Ratatosk corrects long read errors using a de Bruijn graph and accurate short reads, improving variant calling and assembly accuracy.

This study benchmarks small variant detection using ONT long-read sequencing, showing high performance in challenging genomic regions compared to short-read sequencing.

Bifrost constructs and indexes colored and compacted de Bruijn graphs efficiently for large genomic datasets, reducing memory usage and processing time.