ARCS: scaffolding genome drafts with linked reads. - Sarah Yeo; Lauren Coombe; René L. Warren; Justin Chu; Inanç Birol (Bioinform., 2018)

ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers. - Lauren Coombe; Jessica Zhang; Benjamin P. Vandervalk; Justin Chu; Shaun D. Jackman; Inanç Birol; René L. Warren (BMC Bioinform., 2018)

Tigmint: correcting assembly errors using linked reads from large molecules. - Shaun D. Jackman; Lauren Coombe; Justin Chu; René L. Warren; Benjamin P. Vandervalk; Sarah Yeo; Zhuyi Xue; Hamid Mohamadi; Jörg Bohlmann; Steven J. M. Jones; Inanç Birol (BMC Bioinform., 2018)

ntEdit: scalable genome sequence polishing. - René L. Warren; Lauren Coombe; Hamid Mohamadi; Jessica Zhang; Barry Jaquish; Nathalie Isabel; Steven J. M. Jones; Jean Bousquet; Jörg Bohlmann; Inanç Birol (Bioinform., 2019)

ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs. - Lauren Coombe; Vladimir Nikolic; Justin Chu; Inanç Birol; René L. Warren (Bioinform., 2020)

LongStitch: high-quality genome assembly correction and scaffolding using long reads. - Lauren Coombe; Janet X. Li; Theodora Lo; Johnathan Wong; Vladimir Nikolic; René L. Warren; Inanç Birol (BMC Bioinform., 2021)

RResolver: efficient short-read repeat resolution within ABySS. - Vladimir Nikolic; Amirhossein Afshinfard; Justin Chu; Johnathan Wong; Lauren Coombe; Ka Ming Nip; René L. Warren; Inanç Birol (BMC Bioinform., 2022)

btllib: A C++ library with Python interface for efficient genomic sequence processing. - Vladimir Nikolic; Parham Kazemi; Lauren Coombe; Johnathan Wong; Amirhossein Afshinfard; Justin Chu; René L. Warren; Inanç Birol (J. Open Source Softw., 2022)

GoldPolish-target: targeted long-read genome assembly polishing. - Emily Zhang; Lauren Coombe; Johnathan Wong; René L. Warren; Inanç Birol (BMC Bioinform., 2025)