New Tutorial: VGP assembly pipeline

new tutorial assembly pacbio vgp

Posted on: 14 March 2022 purlPURL: 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

Feedback: Easy slide recordings

21 November 2023   feedback testimonial gtn

I recently imported Friends Don’t Let Friends Make Bad Graphs, a fantastic and educational github repository showcasing some common visualisation mistakes, that was available under an open license, to the GTN. Then the GTN automatically made a video for me.

GTN has left Twitter/X as of October

21 November 2023   gtn communications

We did not formally announce it at the time, but the Galaxy Training Network has migrated from Twitter/X to Mastodon, as that platform no longer aligns with the Galaxy Project Code of Conduct nor our community values.

Single cell subdomain re-launch: Unified and feedback-driven

12 October 2023   gtn singlecell

The European Galaxy Days 2023 CoFest combined the forces of administrator, developer and trainer to update and re-launch the single cell Galaxy instance. Where previously there were two subdomains each with their own sets of tools, there is now a unified subdomain with re-categorized tools that makes sense for users.

New Feature: Embeddable GTN Tutorial Lists and UseGalaxy Workflow List Widgets

5 October 2023   new feature gtn

We at the GTN strive to bring you the most fun and fancy features we can in a completely static site! Today we’re addressing the question of Wendi Bacon who needed a solution for keeping her single cell subdomain up-to-date with all the latest happenings in the Single Cell world.