Our list of software and pipelines

VGP genome assembly pipeline

Suite of tools and scripts for assembling high-quality genomes following the VGP 1.5-2.0 genome assembly pipeline originally published in Rhie et al., Nature 2021.

VGP Galaxy pipeline

VGP 2.0 genome assembly pipeline implemented in Galaxy.


Pipeline to assemble full mitochondria genomes from raw PacBio CLR or Oxford Nanapore data as published in Formenti et al., Genmome Biology 2021.


k-mer based variant-filtering algorithm for improved accuracy in genotyping and genome assembly polishing.


Tool for converting, evaluate and manipulate genome sequences using assembly graphs in GFA format.

Gnome Seeker

Small tool to fetch genome vertebrate assemblies from NCBI, group them by taxonomic classes and collect their assembly statistics.

Other tools we helped develop


Tool for resolving haploid switching issue in diploid genome assemblies as published in Kornenberg et al., Nature Cmmunications 2021.


We contributed to the development of a new feature of hifiasm that uses HiC data and PacBio Hifi reads to resolve haplotypes without the use of parental data as published in Cheng et al., Nature Biotechnology 2022.