buisciii/plasmidid repository overview

docker run buisciii/plasmidid plasmidID.sh \
     -1 TEST_DATA/KPN_TEST_R1.fastq.gz  \
     -2 TEST_DATA/KPN_TEST_R2.fastq.gz \
     -d TEST_DATA/plasmids_TEST_database.fasta \
     -c TEST_DATA/contigs_KPN_TEST.fasta \
     --no-trim \ 
     -s KPN

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