Workflows

Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury. Part of the VGP pipeline.

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 ...

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.

Generate Nx and Size plot for multiple assemblies

Inputs

Collection of fasta files. The name of each item in the collection will be used as label for the Nx and Size plots.

Outputs

1. Nx plot
2. Size plot

Microbiome - Variant calling and Consensus Building

Build a consensus sequence from FILTER PASS variants with intrasample allele-frequency above a configurable consensus threshold. Hard-mask regions with low coverage (but not consensus variants within them) and ambiguous sites.