Assembly of bacterial paired-end short read data with generation of quality metrics and reports

Short paired-end read analysis to provide quality analysis, read cleaning and taxonomy assignation

Scaffolding with Bionano

Scaffolding using Bionano optical map data

Inputs

1. Bionano data [cmap]
2. Estimated genome size [txt]
3. Phased assembly generated by Hifiasm [gfa1]

Outputs

1. Scaffolds
2. Non-scaffolded contigs
3. QC: Assembly statistics
4. QC: Nx plot
5. QC: Size plot

This workflow

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

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

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.