Luiz C. Irber

The paper introduces branchwater, a tool for fast petabase-scale sequence search across public metagenomes using FracMinHash k-mer sketching.

The paper identifies five bacterial strains associated with Crohn's disease using a novel method combining machine learning and assembly graphs for metagenomic analysis.

This paper introduces a method using protein k-mers to perform metapangenomics without assembly, identifying strain fluctuations in stool metagenomes during antibiotic treatment.

The paper evaluates metagenomic software tools using realistic datasets, highlighting improvements in assembly and taxon profiling while identifying remaining challenges in virus/archaea detection and reproducibility.

Greedy minimum set cover over FracMinHash k-mer sketches selects a small set of reference genomes explaining a metagenome, supporting species-level taxonomic profiling and choice of genomes for read mapping.

The paper provides strategies for using workflow systems to streamline biological data analysis, emphasizing reproducibility and scalability in high-throughput sequencing projects.

The paper introduces sourmash, a software package that uses MinHash to create compressed sequence signatures for efficient large-scale sequence comparison and database searching.

The paper evaluates metagenome assemblers on a mock community with 64 genomes, finding MEGAHIT performs best and recovers more strain variants.

The paper introduces an open-source implementation of the HyperLogLog algorithm for efficiently estimating k-mer counts in large DNA sequencing datasets.