Execution

Usage

plasmidID.sh -1 <R1> -2 <R2> -d <database(fasta)> -s <sample_name> [-g group_name] [options]
	Mandatory input data:
	-1 | --R1	<filename>	reads corresponding to paired-end R1 (mandatory)
	-2 | --R2	<filename>	reads corresponding to paired-end R2 (mandatory)
	-d | --database	<filename>	database to map and reconstruct (mandatory)
	-s | --sample	<string>	sample name (mandatory)

	Optional input data:
	-g | --group	<string>	group name (optional). If unset, samples will be gathered in NO_GROUP group
	-c | --contig	<filename>	file with contigs. If supplied, plasmidID will not assembly reads
	-a | --annotate <filename>	file with sequences to draw in the final images
	-o 		<output_dir>	output directory, by default is the current directory

	Pipeline options:
	-C | --coverage-cutoff	<int>	minimun coverage percentage to select a plasmid as scafold (0-100), default 80
	-S | --coverage-summary	<int>	minimun coverage percentage to include plasmids in summary image (0-100), default 90
	-f | --cluster		<int>	identity percentage to cluster plasmids into the same representative sequence (0-100), default 80
	-i | --alignment-identity <int>	minimun identity percentage aligned for a contig to annotate
	-l | --alignment-percentage <int>	minimun length percentage aligned for a contig to annotate
	-L | --length-total	<int>	minimun alignment length to filter blast analysis

	--explore	Relaxes default parameters to find less reliable relationships within data supplied and database
	--no-trim	Reads supplied will not be quality trimmed
	--only-reconstruct	Database supplied will not be filtered and all sequences will be used as scaffold 
	
	Additional options:

	-M | --memory	<int>	max memory allowed to use
	-T | --threads	<int>	number of threads
	-v | --version		version
	-h | --help		display usage message

Examples

Relaunch PlasmidID

Relaunch PlasmidID with different parameters is easy and faster. PlasmidID look for the most 'expensive' files and, if they exist, it skip the creation process, since they does not need to be executed again to obtain different results. Images and alignment files might be overwritten though, so making a copy is advised.