Generic variation analysis reporting

This workflow generates reports from a list of variants generated by Variant Calling Workflow.

The workflow accepts a single input:

• A collection of VCF files

The workflow produces two outputs (format description below):

1. A list of variants grouped by Sample
2. A list of variants grouped by Variant

Here is example of output by sample. In this table all varinats in all samples are epxlicitrly listed:

| Sample | ...

Generic variant calling

A generic workflow for identification of variants in a haploid genome such as genomes of bacteria or viruses. It can be readily used on MonkeyPox. The workflow accepts two inputs:

• A genbank file with the reference genomes
• A collection of paired fastqsanger files

The workflow outputs a collection of VCF files for each sample (each fastq pair). These VCF files serve as input to the Reporting workflow.

Workflow can be accessed ...

Performs Long Read assembly using PacBio data and Hifiasm. Part of VGP assembly pipeline. This workflow generate a phased assembly.

Performs scaffolding using HiC Data. Part of VGP assembly pipeline. The scaffolding can be performed on long read assembly contigs or on scaffolds (e.g.: Bionano scaffolds).

Performs scaffolding using Bionano Data. Part of VGP assembly pipeline.

Purge Phased assembly of duplications and overlaps. Include purge steps for Primary and Alternate assemblies.

Performs Long Read assembly using PacBio data and Hifiasm. Part of VGP assembly pipeline. This workflow generate a phased assembly.

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

RNA-RNA interactome analysis using ChiRA tools suite. The aligner used is CLAN.

RNA-RNA interactome analysis using ChiRA tools suite. The aligner used is BWA-MEM.