Kristoffer Sahlin

This paper introduces hybrid RY-mers to improve aDNA alignment sensitivity and efficiency, showing higher accuracy and reduced runtime compared to existing methods.

The paper derives a formula (Z-value) to predict contig length from read length, coverage, and genome properties, showing high accuracy and practical applications for assembler choice and experimental design.

synpact improves PacBio HiFi read mapping accuracy while reducing memory usage and increasing speed compared to existing mappers.

The paper introduces multi-context seeds to improve read mapping accuracy while maintaining speed and memory efficiency.

AEMB improves metagenomic binning efficiency by reducing computational demands while maintaining binning accuracy.

cONcat reconstructs concatenated DNA fragments from Oxford Nanopore reads by matching fragments to reads using edit distance, showing accuracy for short fragments but challenges with read start errors.

isONclust3 clusters large long-read transcriptome datasets into gene families more efficiently than existing tools, achieving comparable or better results.

This paper introduces new randstrobe construction methods, identifies biases in previous approaches, and improves accuracy in short-read mapping.

The paper analyzes transcript isoform diversity of Y-chromosomal ampliconic genes in six great ape species using long-read sequencing and identifies evolutionary patterns and pseudogenization trends.

mapquik accelerates long-read mapping by using minimizer-space seeding and a pseudo-chaining algorithm, achieving high sensitivity and speed on human and maize genomes.

The paper shows that seed entropy predicts sensitivity in sequence matching and introduces new strobemer constructs that improve sensitivity and accuracy.

This paper develops a bioinformatics pipeline using Oxford Nanopore sequencing to reconstruct multi-copy gene families, demonstrating its effectiveness in handling PCR-induced recombination and providing reliable haplotype information.

This paper introduces a new read aligner, strobealign, that uses dynamic fuzzy seeds to achieve faster and more accurate alignment than existing tools.

This paper surveys long-read mapping algorithms, highlighting their evolution from seed-and-extend to seed-and-chain frameworks and introduces a visualization tool for parameter settings.

The paper introduces strobemers as an alternative to k-mers for sequence comparison, showing they are less sensitive to mutation rates and provide better match coverage.

uLTRA improves long-read RNA sequencing alignment accuracy using a two-pass collinear chaining algorithm, outperforming existing tools on simulated and biological data.

The paper introduces isONcorrect, a method to error correct Oxford Nanopore cDNA data, enabling reference-free transcriptome analysis with high accuracy.

The paper introduces isONclust, a greedy, quality-value based algorithm for clustering long-read transcriptome data, showing improved accuracy and scalability over existing methods.

IsoCon improves transcript reconstruction of highly similar multigene family transcripts using long-read sequencing, detecting rare variants and novel isoforms in Y ampliconic gene families.

The paper improves genome scaffolding by addressing PE-contamination in mate-pair libraries using an ILP-based approach in the BESST scaffolder, showing significant quality improvements.

The paper improves structural variation detection by introducing a more accurate null hypothesis, reducing false positives and correcting a bias in variant calling.