Using:

• vadr annotation (model to select)
• vardict variant caller
• coverage depth

Provides summarizing files:

• png image of variant calling with annotations and coverage depths
• tsv file with all information of significant variants only
• vcf file with all information of significant variants only (to allow downstream NextStrain analyses)

Using:

• vadr annotation (model to select)
• vardict variant caller
• coverage depth

Provides summarizing files:

• png image of variant calling with annotations and coverage depths
• tsv file with all information of significant variants only
• vcf file with all information of significant variants only (to allow downstream NextStrain analyses)

Using:

• vadr annotation (model to select)
• vardict variant caller
• coverage depth

Provides summarizing files:

• png image of variant calling with annotations and coverage depths
• tsv file with all information of significant variants only
• vcf file with all information of significant variants only (to allow downstream NextStrain analyses)

Using:

• vadr annotation (model to select)
• vardict variant caller
• coverage depth

Provides summarizing files:

• png image of variant calling with annotations and coverage depths
• tsv file with all information of significant variants only
• vcf file with all information of significant variants only (to allow downstream NextStrain analyses)

Shotgun Metagenomics Analysis

Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more

Description

The input for this analysis is paired end next generation sequencing data from metagenomic samples. The workflow is designed to be modular, so that individual modules can be run depending on the nature of the metagenomics project at hand. More modules will be added as we develop them - this repo is a work in progress!

These scripts have been written ...