Workflows

This workflow performs taxonomic classification of an input sequence collection (e.g., bins from SemiBin2 or MetaBat) using GTDB-Tk and maps the resulting taxonomy to NCBI taxIDs and names to reconcile differences between classification systems.

Purge contigs marked as duplicates by purge_dups in a single haplotype (could be haplotypic duplication or overlap duplication). If you think the purged contigs might belong to the other haplotype, use the workflow VGP6 instead. 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).

Purge contigs marked as duplicates by purge_dups.

This workflow starts from metagenomics short-read data and performs, taxonomic profiling (using Sylph), predicts Antibiotic Resistance Genes (ARGs) (using Groot and deepARG), and standardizes ARG annotations (using argNorm).

This workflow performs core genome multilocus sequence typing (cgMLST) on contigs corresponding to one bacterial genome to characterize bacterial strains using curated reference schemes.

This workflow performs genome annotation using Braker3 and evaluates the quality of the annotation with BUSCO and genome annotation statistics.

This workflow takes Nanopore fastq(.gz) files and runs Minimap2 to map the reads against a reference genome (human, by default). It filters the output to keep only the unmapped reads and generates mapping statistics that are aggregated into a MultiQC report.

This workflow takes paired-end Illumina fastq(.gz) files and runs Bowtie to map the reads against a reference genome (human, by default) and keep only the reads that do not align. MultiQC is used to aggregate the mapping reports.

This workflow performs quality control and trimming on paired-end Illumina fastq(.gz) files using fastp and aggregates the quality control reports with MultiQC

Metagenomic analysis, from raw reads to gene catalog. Uses Megahit to assemble contigs and Prodgial to predict CDSs on contigs to provide the gene catalog. Finally, functional, taxonomic, and antimicrobial resistance information is provided.