Syntax
This tool reconstructs individual plasmid sequences from draft genome assemblies using the plasmid reference databases.
For more information please visit https://github.com/phac-nml/mob-suite/.
Workflow
This preliminary "Mobilome and Resistome Analysis Workflow" linking mob_recon with staramr provides reports on mobilome and resistome for a given isolate given a draft genome assembly. The workflow is located in Shared Data --> Workflows --> Mobilome and Resistome Analysis Workflow (MOB-Recon and STARAMR). The workflow file can also be manually downloaded from https://raw.githubusercontent.com/phac-nml/galaxy_tools/master/tools/mob_suite/workflows/AMRworkflow_STARAMR.ga.
Input:
A FASTA file with a single or multiple contigs (e.g. a draft genome assembly):
Output:
Tab-delimited report listing information for each input contig on its cluster number, possible replicon, relaxase, and repetitive elements types, etc. Refer to https://github.com/phac-nml/mob-suite#mob-recon-contig-report-format for the description of each column.
Note: Plasmid sequences will not be output if none are found. Some plasmid could be intergrated into a chromosome.