Bacannot - A generic genome annotation pipeline for prokaryotes

Designed to provide an easy-to-use framework for performing a comprehensive annotation on prokaryotic genomes, bacannot is developed with Nextflow and Docker. It can annotate resistance genes, virulence factors, genomic islands, prophages, methylation and more.

Its main steps are:

Analysis steps Used software or databases
Genome assembly (if raw reads are given) Flye and Unicycler
Generic annotation and gene prediction Prokka
rRNA prediction barrnap
Classification within multi-locus sequence types (STs) mlst
KEGG KO annotation and visualization KofamScan and KEGGDecoder
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
In silico detection of plasmids Plasmidfinder and Platon
Prediction and visualization of genomic islands IslandPath-DIMOB and gff-toolbox
Merge of annotation results bedtools
Renderization of results in a Genome Browser JBrowse
Renderization of automatic reports and shiny app for results interrogation R Markdown and Shiny

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