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.
mitoVGP
Pipeline to assemble full mitochondria genomes from raw PacBio CLR or Oxford Nanapore data as published in Formenti et al., Genmome Biology 2021.
Merfin
k-mer based variant-filtering algorithm for improved accuracy in genotyping and genome assembly polishing.
GFastats
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
FALCON-phase
Tool for resolving haploid switching issue in diploid genome assemblies as published in Kornenberg et al., Nature Cmmunications 2021.
Hifiasm
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.