Workflows

This workflow

• Reconstruct phylogeny (insert fragments in a reference)
• Alpha rarefaction analysis
• Taxonomic analysis

Microbiome - Variant calling and Consensus Building

Nanopore datasets analysis - Phylogenetic Identification - antibiotic resistance genes detection and contigs building

Microbiome - QC and Contamination Filtering

Pathogens of all samples report generation and visualization

Microbiome - Taxonomy Profiling

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

This workflow takes a collection of BAM (output of STAR) and a gtf. It extends the input gtf using de novo annotation.

Annotation of an assembled bacterial genomes to detect genes, potential plasmids, integrons and Insertion sequence (IS) elements.

Antimicrobial resistance gene detection from assembled bacterial genomes