Workflows

Overview


The Vertebrate Genomes Pipelines in Galaxy are intended to allow a user to generate high-quality near error-free assemblies of species from a user's own data or from the GenomeArk database. Depending on the available data, different versions of this workflow are available.

Link Workflow Inputs Outputs
Dockstore MerylDB generation:
Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury.
ILL-PE
1. Hifi long reads [fastq] 1. Meryl Database of kmer counts
2. GenomeScope summary, models and plots
Dockstore MerylDB generation Trio:
Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury using parental and offspring datasets
ILL-PE
1. Hifi long reads [fastq]
2. Paternal short-read Illumina sequencing reads [fastq]
3. Maternal short-read Illumina sequencing reads [fastq]
1. Meryl Database of kmer counts
2. GenomeScope summary, models and plots