Workflows

This workflow performs functional annotation of protein and nucleotide sequences (including CDS, genomes and metagenomes) using eggNOG-mapper and InterProScan, supports collection inputs and optional analysis steps, and can assess KEGG pathway completeness.

This workflow performs automated, parallel annotation of metagenome-assembled genomes (MAGs) to generate standardized annotation outputs, merged summary tables, and integrated quality reports across all genomes.

Generate a genome assembly based on PacBio HiFi reads. Part of the VGP suite, it needs to be run after the VGP1 k-mer profiling workflow. The assembly contigs are built using HiFiasm, and the workflow generates assembly statistics, BUSCO reports, Merqury plots, and the contigs in fasta and GFA formats.

This workflow performs variant and genotype calling on whole-genome paired-end sequencing data from organisms of any ploidy to produce annotated VCF and TSV files

Runs CAPHEINE selection analyses with optional foreground/background branch labeling for branch comparisons.

This workflow performs the scaffolding of a genome assembly using HiC data with YAHS. Can be used on any assembly with Hi-C data, and the assembly in the gfa format.

Evaluation of Pacbio Hifi Reads and genome profiling. Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury. Part of the VGP pipeline.

This workflow performs multi-algorithm metagenomic binning evaluation using CONCOCT, MetaBAT2, SemiBin, and MaxBin2, optimizes results with DAS Tool and Binette, and evaluates all binning outputs against a gold standard using the CAMI AMBER framework to generate comprehensive HTML reports and performance metrics.

This workflow performs taxonomic classification of an input sequence collection (e.g., bins from SemiBin2 or MetaBat) using GTDB-Tk and maps the resulting taxonomy to NCBI taxIDs and names to reconcile differences between classification systems.

Purge contigs marked as duplicates by purge_dups in a single haplotype (could be haplotypic duplication or overlap duplication). If you think the purged contigs might belong to the other haplotype, use the workflow VGP6 instead. This workflow is the 6th workflow of the VGP pipeline. It is meant to be run after one of the contigging steps (Workflow 3, 4, or 5).