These are the tools that wrapped inside bacannot. Cite the tools whenever you use its output.
| Analysis steps | Used software or databases |
|---|---|
| Genome assembly (if raw reads are given) | Flye and Unicycler |
| Identification of closest 10 NCBI Refseq genomes and comparison of genomes | RefSeq Masher and Sourmash |
| 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 |