COVID-19: variation analysis on ARTIC PE data

The workflow for Illumina-sequenced ampliconic data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but adds extra logic for trimming amplicon primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by primer-binding site mutations and, if possible, excludes reads derived from such ...

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

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