PANDAseq: paired-end assembler for illumina sequences. - Andre P. Masella; Andrea K. Bartram; Jakub Truszkowski; Daniel Gregory Brown; Josh D. Neufeld (BMC Bioinform., 2012)

Pygenprop: a Python library for programmatic exploration and comparison of organism genome properties. - Lee H. Bergstrand; Josh D. Neufeld; Andrew C. Doxey (Bioinform., 2019)

AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods. - Xin Wei; Huagang Tan; Briallen Lobb; William Zhen; Zijing Wu; Donovan H. Parks; Josh D. Neufeld; Gabriel Moreno-Hagelsieb; Andrew C. Doxey (Briefings Bioinform., 2024)