Josipa Lipovac

This study evaluates Sourmash's ability to profile microbial strains from long-read metagenomes, showing accurate gene content recovery and abundance estimation.

StrainRefine improves strain-level metagenomic classification by refining read mappings using profile similarity, reducing false positives while maintaining accuracy.

T2T-HG002v1.1, a complete diploid HG002 assembly lacking detectable errors over 99.4% of its length, enables genome-based benchmarking of assemblies, sequencing reads, and phased variant calls.

MADRe improves strain-level metagenomic classification by combining assembly-driven database reduction with probabilistic read mapping, achieving higher precision and fewer false positives than existing tools.

The paper presents a high-quality, gapless diploid reference genome for an Indian population, revealing extensive structural variation and improved performance for genomic analysis in South Asian samples.

This study evaluates optimal long-read data types and volumes for chromosome-level haplotype-resolved pangenome assembly, providing guidelines for sequencing platform selection and coverage.