A universal genomic coordinate translator for comparative genomics. - Neda Zamani; Görel Sundström; Jennifer R. S. Meadows; Marc P. Höppner; Jacques Dainat; Henrik Lantz; Brian J. Haas; Manfred G. Grabherr (BMC Bioinform., 2014)

GUESSmyLT: Software to guess the RNA-Seq library type of paired and single end read files. - Erik Wik; Hampus Olin; Caitlin Haughey; Lisa Klasson; Jacques Dainat (J. Open Source Softw., 2019)

Baargin: a Nextflow workflow for the automatic analysis of bacterial genomics data with a focus on Antimicrobial Resistance. - Juliette Hayer; Jacques Dainat; Ella Marcy; Anne-Laure Bañuls (J. Open Source Softw., 2023)

AliNe: A Flexible and Efficient Nextflow Pipeline for Read Alignment. - Jacques Dainat (J. Open Source Softw., 2025)