A tool to reconstruct plasmids in bacterial assemblies
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
fasta{:bash}
:file
A bacterial genome assembly in FASTA format
*.{fasta,fa,fna}
chromosome{:bash}
results/chromosome.fasta{:bash}
FASTA file of all contigs found to belong to the chromosome
chromosome.fasta
contig_report{:bash}
results/contig_report.txt{:bash}
Assignment of the contig to chromosome or a particular plasmid grouping
contig_report.txt
plasmids{:bash}
results/plasmid_*.fasta{:bash}
Each plasmid group is written to an individual FASTA
plasmid_*.fasta
mobtyper_results{:bash}
results/mobtyper_results.txt{:bash}
Aggregate MOB-typer report files for all identified plasmid
mobtyper_results.txt
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Software tools for clustering, reconstruction and typing of plasmids from draft assemblies.
