vgp-assembly

VGP repository for the genome assembly working group

Contents

• Galaxy Workflow
• DNAnexus Workflow
• Docker images with WDL Workflow
• Pipeline for local run
• MitoVGP pipeline
• Instructions for AWS s3 genomeark
• Meta data
• Citation

Galaxy Workflow

Starting the VGP v2.0 pipeline, the production has been moved to the Galaxy environment. The major difference from the Rhie et al. 2021 is the replacement of the CLR component to HiFi and additional options for QCing and Hi-C scaffolding.

• Tutorials: starting point for new trainees
• Workflows: dockstore workflow, input, and output for each assembly steps

DNAnexus Workflow

The production of the VGP v1.0-1.1 assemblies has been performed on DNAnexus, which is available for anyone that registers. We welcome new trainees who are interested in leading the assembly of VGP and other genomes. Feel free to contact us.

• Tutorials: starting point for new trainees
• Workflows: workflow to run each assembly steps
• Applets: individual applets in the workflow
• Retrieve job info

Docker images with WDL Workflow

The scaffolding pipeline to run on generic architecture and Docker containers is available to the public. This includes a WDL implementation of the scaffolding portion of VGP Assembly, as well as some of the QC steps. Note that Falcon assembly and Arrow polishing are not included.

• WDL Pipeline: read the manual first

Pipeline for local run

The local pipeline is available for each individual step for scaffolding, polishing, and evaluation as bash scripts. These scripts were used to locally assemble the first 17 genomes described in Rhie et al. 2021.

Note the scripts are optimized to run on a Slurm schedular and tested on Biowulf. All submitter scripts have a prefix of _submit_.

• Pipeline

MitoVGP pipeline

Pipeline for generating mitochondrial sequences is available on a conda release.

• MitoVGP

Instructions for AWS s3 genomeark

This is only relevant for our collaborators and data managers, for sharing sequencing data on genomeark not produced by VGP.

• Upload to genomeark
• Symlink s3 objects to DNAnexus
• Data structure on AWS genomeark and DNAnexus

Meta data

The meta data proposal and specifications. Actual meta data is stored in this repository.

• Proposal
• Specimen naming scheme

Citation

• VGP assemblies and genome assembly pipeline: Rhie et al., Towards complete and error-free genome assemblies of all vertebrate species, Nature 2021. doi: https://doi.org/10.1038/s41586-021-03451-0

• Mitochondrial genome assembly pipeline: Formenti et al., Complete vertebrate mitogenomes reveal widespread repeats and gene duplications, Genome Biology 2021. doi: https://doi.org/10.1186/s13059-021-02336-9