Bandage: interactive visualization of de novo genome assemblies. - Ryan R. Wick; Mark B. Schultz; Justin Zobel; Kathryn E. Holt (Bioinform., 2015)

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. - Ryan R. Wick; Louise M. Judd; Claire L. Gorrie; Kathryn E. Holt (PLoS Comput. Biol., 2017)

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks. - Ryan R. Wick; Louise M. Judd; Kathryn E. Holt (PLoS Comput. Biol., 2018)

Badread: simulation of error-prone long reads. - Ryan R. Wick (J. Open Source Softw., 2019)

Polypolish: Short-read polishing of long-read bacterial genome assemblies. - Ryan R. Wick; Kathryn E. Holt (PLoS Comput. Biol., 2022)

Perfecting bacterial genome assembly. - Ryan R. Wick (2022)

Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing. - Ryan R. Wick; Louise M. Judd; Kathryn E. Holt (PLoS Comput. Biol., 2023)