Welcome to bacannot pipeline documentation
About
Bacannot is a pipeline designed to provide an easy-to-use framework for performing a comprehensive annotation on prokaryotic genomes. It is developed with Nextflow and Docker. It can annotate resistance genes, virulence factors, genomic islands, prophages, methylation and more.
Workflow
The pipeline's main steps are:
| Analysis steps | Used software or databases |
|---|---|
| Genome assembly (if raw reads are given) | Flye and Unicycler |
| Identification of closest 10 NCBI Refseq genomes | RefSeq Masher |
| Generic annotation and gene prediction | Prokka or Bakta |
| rRNA prediction | barrnap |
| Classification within multi-locus sequence types (STs) | mlst |
| KEGG KO annotation and visualization | KofamScan and KEGGDecoder |
| Annotation of secondary metabolites | antiSMASH |
| Methylation annotation | Nanopolish |
| Annotation of antimicrobial (AMR) genes | AMRFinderPlus, ARGminer, Resfinder and RGI |
| Annotation of virulence genes | Victors and VFDB |
| Prophage sequences and genes annotation | PHASTER, Phigaro and PhySpy |
| Annotation of integrative and conjugative elements | ICEberg |
| Annotation of bacterial integrons | Integron Finder |
| Focused detection of insertion sequences | digIS |
| In silico detection and typing of plasmids | Plasmidfinder, Platon and MOB-typer |
| Prediction and visualization of genomic islands | IslandPath-DIMOB and gff-toolbox |
| Custom annotation from formatted FASTA or NCBI protein IDs | BLAST |
| Merge of annotation results | bedtools |
| Genome Browser renderization | JBrowse |
| Circos plot generation | easy_circos |
| Renderization of automatic reports and shiny app for results interrogation | R Markdown, Shiny and SequenceServer |
Quickstart
A quickstart is available so you can quickly get the gist of the pipeline's capabilities.
About prokka annotation
In order to increase the accuracy of prokka annotation, this pipeline includes an additional HMM database to prokka's defaults. It can be either TIGRFAM (smaller but curated) or PGAP (bigger comprehensive NCBI database that contains TIGRFAM).
Usage
The pipeline's common usage is very simple as shown below:
# usual command-line
nextflow run fmalmeida/bacannot \
--bacannot_db "./bacannot_databases" \
--input "bacannot_samplesheet.yml"
Quote
Some parameters are required, some are not. Please read the pipeline's manual reference to understand each parameter.
Support contact
Whenever a doubt arise feel free to contact me at almeidafmarques@gmail.com