Matthew Z. DeMaere

Rhometa estimates population recombination rates from metagenomic read datasets using a composite likelihood approach, showing accuracy with 80 genomes and real experimental data.

The paper introduces a reference-free quality control method for Hi-C sequencing data, demonstrating its accuracy on simulated and real datasets.

The paper introduces bin3C, an unsupervised method using Hi-C data to resolve MAGs from a single time-point, validated against simulated data and compared to ProxiMeta.

CAMISIM simulates microbial communities and metagenomes with truth standards, enabling benchmarking of metagenomic analysis tools.

Sim3C simulates HiC and Meta3C sequencing data by modeling genomic spatial structures and errors, aiding in algorithm testing and experimental design.

The paper benchmarks computational metagenomics software using complex datasets, showing strengths and limitations in assembly, binning, and taxonomic profiling.

The paper evaluates ddRADseq for reduced representation metagenome sequencing, finding it feasible with small taxonomic bias compared to DNA extraction bias.