This workflow constructs Metagenome-Assembled Genomes (MAGs) using SPAdes or MEGAHIT as assemblers, followed by binning with four different tools and refinement using Binette. The resulting MAGs are dereplicated across the entire input sample set, then annotated and evaluated for quality. You can provide pooled reads (for co-assembly/binning), individual read sets, or a combination of both. The input samples must consist of the original reads, which are used for abundance estimation. In all cases, ...

This workflow can be used to assign multi-element molecular formulas to ultrahigh resolution mass spectra.

Workflow to predict EI mass spectra using QCxMS starting from a single SDF file, containing the 3D coordinates of all atoms in the molecule. These files can typically be obtained from PubChem.

Perform dcTMD free energy simulations and calculations

Complete multiplex tissue image (MTI) analysis pipeline for tissue microarray (TMA) data imaged using cyclic immunofluorescence: Performs illumination correction, stitching and registration, and tissue microarray segmentation. Tissue-segmented images undergo nuclear segmentation, cell/nuclei feature quantification (mean marker intensities, cell coordinates, and morphological features), and cell phenotyping. Produces outputs that are compatible with downstream single-cell/spatial analysis and ...

Decontamination Workflow

Decontamination (foreign contaminants and mitochondrial sequences) of genome assembly after scaffolding step. Part of the VGP Suite.

Inputs

• Genome Assembly [fasta]
• Database for Kraken2. Database containing the possible contaminants.

Ouput

• List of contaminant scaffolds
• List of mitochondrial scaffolds
• Decontaminated assembly

This workflow perform the scaffolding of a genome assemble using HiC data with YAHS. Part of the VGP set of workflows.

This workflow generates Hi-C contact maps for genome assemblies in the Pretext format. It is compatible with one or 2 haplotypes. It includes tracks for PacBio read coverage, Gaps, and telomeres. The Pretext files can be open in PretextView for the manual curation of genome assemblies.

Genome Assembly with Hifi reads and Trio Data

Generate phased assembly based on PacBio Hifi Reads using parental Illumina data for phasing. Part of the VGP workflow suite, it needs to be run after the Trio k-mer Profiling workflow VGP2.

Inputs

1. Hifi long reads [fastq]
2. Concatenated Illumina reads : Paternal [fastq]
3. Concatenated Illumina reads : Maternal [fastq]
4. K-mer database [meryldb] generated by VGP2 workflow.
5. Paternal hapmer database [meryldb] generated by VGP2 workflow.

...

Purge contigs marked as duplicates by purge_dups (could be haplotypic duplication or overlap duplication). 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)