New Tutorial: VGP assembly pipeline

Author(s) orcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoAlex Ostrovsky avatar Alex Ostrovsky
new tutorial assembly pacbio vgp

Posted on: 14 March 2022 PURL: https://gxy.io/GTN:N00033

We are proud to announce that, as result of the collaboration with the Vertebrate Genomes Project (VGP), a new training describing the VGP assembly pipeline is now available in the Galaxy Training Network. The Vertebrate Genomes Project aims to generate high-quality, near-error-free, gap-free, chromosome-level, haplotype-phased, annotated reference genome assemblies for every vertebrate species.

VGP pipeline. Open image in new tab

Figure 1: VPG Pipeline 2.0. The pipeline starts with assembly of the HiFi reads into contigs, yielding the primary and alternate assemblies. Then, duplicated and erroneously assigned contigs will be removed by using purge_dups. Finally, Bionano optical maps and HiC data are used to generate a scaffolded primary assembly.

The tutorial organized in four sections: genome profile, HiFi phased assembly, post-assembly pocessing and hybrid scaffolding. During the genome profiling stage, diverse tools based on the analsys of k-mer frequencies are used for infering the properties of the genome. After that, a draft assembly is generated by using high accuracy long-read PacBio HiFi reads. In the third stage, the initial assembly is preprocessed for identifying and reassign allelic contigs. Finally, in the last step the assembed contigs are assembled into scaffolds by using two additional technologies: Bionano optical maps and Hi-C data.

View Material
Assembly of vertebrate genomes

Recent News

See all news

GTN is now integrated with WorkflowHub

2 September 2025   gtn workflowhub workflows fair

Thanks to a collaborative effort between the teams at Galaxy Training Network (GTN), WorkflowHub, and Australian BioCommons, GTN workflows are now registered automatically with WorkflowHub. The existing set of workflows can be viewed here: GTN on WorkflowHub. For every new tutorial that is added to the GTN, any workflows that it contains will now also be pushed to WorkflowHub.

Quantifying Electrophoresis Gel Bands with QuPath and Galaxy

18 August 2025   GTN imaging electrophoresis QuPath Galaxy

Gel Electrophoresis is a staple of molecular biology, providing a way to separate DNA, RNA, or proteins by size and charge. While gels are usually interpreted visually, the ability to quantify band intensities offers much richer insights—allowing researchers to estimate product yields, verify PCR amplification, or assess protein purity.