BCFtools/csq: haplotype-aware variant consequences. - Petr Danecek; Shane A. McCarthy (Bioinform., 2017)

Crumble: reference free lossy compression of sequence quality values. - James K. Bonfield; Shane A. McCarthy; Richard Durbin (Bioinform., 2019)

Identifying and removing haplotypic duplication in primary genome assemblies. - Dengfeng Guan; Shane A. McCarthy; Jonathan Wood; Kerstin Howe; Yadong Wang; Richard Durbin (Bioinform., 2020)

Efficient iterative Hi-C scaffolder based on N-best neighbors. - Dengfeng Guan; Shane A. McCarthy; Zemin Ning; Guohua Wang; Yadong Wang; Richard Durbin (BMC Bioinform., 2021)

Correction to: Efficient iterative Hi-C scaffolder based on N-best neighbors. - Dengfeng Guan; Shane A. McCarthy; Zemin Ning; Guohua Wang; Yadong Wang; Richard Durbin (BMC Bioinform., 2021)

YaHS: yet another Hi-C scaffolding tool. - Chenxi Zhou; Shane A. McCarthy; Richard Durbin (Bioinform., 2023)

MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads. - Marcela Uliano-Silva; João Gabriel R. N. Ferreira; Ksenia Krasheninnikova; Mark L. Blaxter; Nova Mieszkowska; Neil Hall; Peter Holland; Richard Durbin; Thomas Richards; Paul J. Kersey; Peter Hollingsworth; Willie Wilson; et al. (BMC Bioinform., 2023)