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

Support Contact

Whenever a doubt arise feel free to contact me at almeidafmarques@gmail.com