Jesse J. Kerkvliet

Calibrating for absolute microbiome abundances without spike-ins

This paper introduces MGCalibrator, a tool for spike-in free absolute abundance estimation in metagenomics, validated against qPCR and applied to track antibiotic resistance genes in wastewater.

gplasCC: classification and reconstruction of plasmids from short-read sequencing data for any bacterial species

gplasCC classifies and reconstructs plasmids from short-read sequencing data across multiple bacterial species using simplified plasmidEC and species-specific databases.

PlasmidEC and gplas2: An optimised short-read approach to predict and reconstruct antibiotic resistance plasmids in Escherichia coli

This paper introduces plasmidEC and gplas2 to accurately predict and reconstruct antibiotic resistance plasmids in E. coli using short-read sequencing data, outperforming existing methods.

The Bellerophon pipeline, improving de novo transcriptomes and removing chimeras

The paper introduces Bellerophon, a pipeline that improves de novo transcriptome quality by removing chimeric sequences through quality assessment and filtering steps.