Sequencing Vertebrate Diversity

50 species from the VGP assembly catalog

Abramis brama

Acanthisitta chloris

Acanthopagrus latus

Acomys russatus

Alca torda

Amblyraja radiata

Ammospiza caudacuta

Anguilla anguilla

Antennarius maculatus

Apus apus

Argentina silus

Ascidiella aspersa

Aythya ferina

Barbus barbus

Borostomias antarcticus

Bucephala clangula

Callithrix jacchus

Candoia aspera

Carcharodon carcharias

Cervus elaphus

Chelmon rostratus

Chiroxiphia lanceolata

Ciconia maguari

Cnephaeus nilssonii

Coregonus lavaretus

Cottoperca gobio

Cynocephalus volans

Dendropsophus ebraccatus

Diceros bicornis

Dryobates pubescens

Electrona antarctica

Elgaria multicarinata

Equus caballus

Erpetoichthys calabaricus

Eubalaena glacialis

Falco biarmicus

Gadus morhua

Gastrophryne carolinensis

Geotrypetes seraphini

Gobius niger

Grus americana

Harpia harpyja

Heptranchias perlo

Hippopotamus amphibius

Hydrolagus colliei

Hyperoodon ampullatus

Labrus bergylta

Lampetra fluviatilis

Lemur catta

Leucopleurus acutus

Building the Tree of Life

The Vertebrate Genomes Project (VGP) aims to generate near error-free, chromosome-level reference genome assemblies for all ~70,000 extant vertebrate species.

Galaxy provides the computational infrastructure to achieve this at scale, with standardized, reproducible workflows accessible to researchers worldwide.

"95% of the main discoveries that have driven biotechnology came from studying things that were not model organisms at the time." - Giulio Formenti

274 genomes and counting

VGP Workflow Modules

Click image to view fullscreen

Pre-Assembly & Assembly

HiFi reads Species name Genetic code

VGP0

Mitogenome Assembly

GenBank file Annotation images

HiFi reads K-mer length Ploidy

VGP1

K-mer Profiling

Meryl database GenomeScope plots

HiFi reads Parental Illumina

VGP2

K-mer Profiling Trio

Meryl DBs GenomeScope profiles

HiFi reads Meryl DB GenomeScope

VGP3

HiFi Assembly

Primary assembly Alternate assembly

HiFi reads HiC reads Meryl DB

VGP4

HiFi+HiC Assembly

Haplotype 1 Haplotype 2

HiFi reads Parental reads Meryl DBs

VGP5

Trio Assembly

Paternal haplotype Maternal haplotype

Post-Assembly Processing

Assemblies Trimmed HiFi Meryl DB

VGP6

Purge Duplicates

Purged primary Purged alternate

Assembly Trimmed HiFi Meryl DB

VGP6b

Purge Single

Purged assembly

Assembly (GFA) Bionano cmap

VGP7

Bionano Scaffolding

Scaffolds QC plots

Assembly (GFA) HiC reads

VGP8

HiC Scaffolding

Scaffolded assembly Contact map

VGP Workflows by Compute

Core hours used by workflows

Top Assembly Tools

Core hours used by individual tools

Peak Memory by Tool

Assembly needs memory!

Powered by Galaxy + ACCESS-CI

VGP leverages the US national cyberinfrastructure through ACCESS-CI, running on resources at TACC (Jetstream2), PSC, NCSA, and SDSC.

This provides the massive memory (up to 4TB) and CPU resources (up to 128 cores) needed for large vertebrate genome assemblies.

Galaxy provides an equivalent of >$2,000,000/year of free computational infrastructure to genomics researchers.

Key VGP Resources

VGP Galaxy vgp.usegalaxy.org GenomeArk genomeark2.org VGP Website vertebrategenomesproject.org Galaxy US usegalaxy.org

gxy.io/what-is-vgp