HmtG-PacBio-Pipeline
Machine-learning workflow (variational autoencoder) that sorts PacBio HiFi mitochondrial reads into parasite haplotypes and species, including mixed infections.
Documentation →Python · R · Galaxy
Software
Tools, pipelines and tutorials I develop or maintain. Most are written in Python and R and are openly available.
PAL2NAL
Codon-based alignment of coding sequences using PAL2NAL.
GitHub →Galaxy · BRC Analytics
BRC Analytics brings reference genomic data for pathogens, hosts and vectors together with Galaxy workflows that run on shared infrastructure. I develop reproducible pathogen-genomics workflows for the project.
brc-analytics.org →Tutorials and workshops
Macro-evolutionary Pangenomics
A Plasmodium case study of pangenome analysis across the monkey-parasite clade.
GitHub →Phylogenetic substitution models
Maximum-likelihood model comparison in orthopoxviruses.
GitHub →Hybrid genome assembly
Hybrid assembly of Leptospira interrogans serovar Copenhageni.
GitHub →