plasmidID1

Overview

plasmidID is a computational pipeline tha reconstruct and annotate the most likely plasmids present in one sample

usage : ./plasmidID <-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), less than 37 characters

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

Pipeline options: --explore Relaxes default parameters to find less reliable relationships within data supplied and database --only-reconstruct Database supplied will not be filtered and all sequences will be used as scaffold

This option does not require R1 and R2, instead a contig file can be supplied

-w

Undo winner takes it all algorithm when clustering by kmer - QUICKER MODE

Trimming: --trimmomatic-directory Indicate directory holding trimmomatic .jar executable --no-trim Reads supplied will not be quality trimmed

Coverage and Clustering: -C | --coverage-cutoff <int> minimum coverage percentage to select a plasmid as scafold (0-100), default 80 -S | --coverage-summary <int> minimum coverage percentage to include plasmids in summary image (0-100), default 90 -f | --cluster <int> kmer identity to cluster plasmids into the same representative sequence (0 means identical) (0-1), default 0.5 -k | --kmer <int> identity to filter plasmids from the database with kmer approach (0-1), default 0.95

Contig local alignment -i | --alignment-identity <int> minimum identity percentage aligned for a contig to annotate, default 90 -l | --alignment-percentage <int> minimum length percentage aligned for a contig to annotate, default 20 -L | --length-total <int> minimum alignment length to filter blast analysis --extend-annotation <int> look for annotation over regions with no homology found (base pairs), default 500bp

Draw images: --config-directory <dir> directory holding config files, default config_files/ --config-file-individual <file-name> file name of the individual file used to reconstruct Additional options:

-M | --memory

<int> max memory allowed to use

-T | --threads

<int> number of threads

-v | --version

version

-h | --help

display usage message

example: ./plasmidID.sh -1 ecoli_R1.fastq.gz -2 ecoli_R2.fastq.gz -d database.fasta -s ECO_553 -G ENTERO

./plasmidID.sh -1 ecoli_R1.fastq.gz -2 ecoli_R2.fastq.gz -d PacBio_sample.fasta -c scaffolds.fasta -C 60 -s ECO_60 -G ENTERO --no-trim