Workflows

Post-curation processing workflow for VGP assemblies. Takes a curated AGP file and combined haplotype FASTA, splits by haplotype, applies curation, assigns chromosome names, renames and reorients hap2 to match hap1, then generates QC outputs including Compleasm, Pretext maps, telomere analysis, and coverage tracks.

This workflow performs colour deconvolution and automated thresholding to quantify stained area in brightfield histological images (MT, IHC). It accepts whole slides or pre-cropped ROIs.

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 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.

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.