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