Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes. mSystems. 5 (2020)

v2.0.2 bactopia/bactopia "Black Mamba" - 2022/02/22 Added bactopia download which merges the bactopia build and bactopia pull commands modules can now use prebuilt envs --available_species to print the species in a bactopia dataset --bbduk_opts to fine tune bbduk set quay as default docker registry Let Nextflow handle stdout and stderr added hpsuissero, legsta, sistr, ssuissero to Merlin Bactopia Tools (bactopia --wf ) amrfinderplus: Identify antimicrobial resistance in genes or proteins abricate: Mass screening of contigs for antimicrobial and virulence genes checkm: Assess the assembly quality of your samples hpsuissero: Serotype prediction of Haemophilus parasuis assemblies kraken2: Taxonomic classification of sequence reads legsta: Typing of Legionella pneumophila assemblies mlst: Scan contig files against PubMLST typing schemes mobsuite: Reconstruct and annotate plasmids in bacterial assemblies rgi: Predict antibiotic resistance from assemblies sistr: Serovar prediction of Salmonella assemblies ssuissero: Serotype prediction of Streptococcus suis assemblies Fixed toInteger on null genome size Index out of bounds in mlst-blast.py (caused by non allele columns) FOFN will fail if sample name is null improve available workflow logic PIRATE not exporting gene_presence_absence.csv correctly channel imports for scoary workflow argument type mismatch when using --use_roary missing channel when agrvate not ran as staphtyper float required options to the top when missing broken tests due to changes bactopia datasets including hidden directories Bioperl pinnings for prokka and pirateIf you use Bactopia, please cite it as below