RCA Pipeline
RCA is a pipeline for the discovery of viruses from Illumina and Nanopore rolling circle amplification data.
Setting up a Conda Environment
The RCA.yml file provided allows for easily setting up a conda environment, which will contain most of the tools needed to run the script.
Ensure that conda is installed and active, and then execute conda env create -f RCA.yml to create and install all tools into the environment.
Please install Ashure separately and update the --ashure_path parameter with the location of the ashure.py file.
Please download the blast database in the ICTV folder and point the --ictv_db parameter to the ICTV_viruses.fasta file.
Please download the adapters.fa the --adapters parameter to this file.
Please activate the conda environment before running the scripts.
Usage:
python Scripts/RCA/rca.py illumina --input Illumina_run/raw_data/ --output Illumina_run/
python Scripts/RCA/rca.py nanopore --input Nanopore_run/raw_data/ --output Nanopore_run/
Illumina Parameters
usage: RCA illumina [-h] --input INPUT --output OUTPUT [--create_dirs {Y,N}]
[--bbduk {Y,N}] [--spades {Y,N}] [--virus_detection {Y,N}]
[--doc_env {Y,N}] [--adapters ADAPTERS]
[--min_len MIN_LEN] [--min_quality MIN_QUALITY]
[--threads THREADS] [--memory MEMORY] [--hmm HMM]
optional arguments:
-h, --help show this help message and exit
--input INPUT This is the location of the raw data directory.
--output OUTPUT This is where the output data will be generated.
--create_dirs {Y,N} Creates the directory structure. Default Y.
--bbduk {Y,N} Runs Bbduk. Default Y.
--spades {Y,N} Runs isONclust. Default Y.
--virus_detection {Y,N}
Extract potential viruses. Default Y.
--doc_env {Y,N} Creates environment and parameter details. Default Y.
--adapters ADAPTERS bbduk adapter references.
--min_len MIN_LEN This is the mininum length of a read allowed by bbduk.
Default 50.
--min_quality MIN_QUALITY
bbduk phred quality trim parameter. Default 10.
--threads THREADS The number of threads to run Spades with. Default 60.
--memory MEMORY The amount of memory, in GB, to run Spades with.
Default 500.
--hmm HMM This is the path to the hmm file.
Nanopore Parameters
usage: RCA nanopore [-h] --input INPUT --output OUTPUT [--ictv_db ICTV_DB]
[--ashure_path ASHURE_PATH] [--create_dirs {Y,N}]
[--ashure {Y,N}] [--isonclust {Y,N}] [--medaka {Y,N}]
[--doc_env {Y,N}] [--threads THREADS]
[--quality_score QUALITY_SCORE]
optional arguments:
-h, --help show this help message and exit
--input INPUT This is the location of the raw data directory.
--output OUTPUT This is where the output data will be generated.
--ictv_db ICTV_DB This is the path to the ictv database fasta file.
--ashure_path ASHURE_PATH
This is the path to the ashure script.
--create_dirs {Y,N} Creates the directory structure. Default Y.
--ashure {Y,N} Runs Ashure. Default Y.
--isonclust {Y,N} Runs isONclust. Default Y.
--medaka {Y,N} Runs medaka. Default Y.
--doc_env {Y,N} Creates environment and parameter details. Default Y.
--threads THREADS The number of threads to run isONclust and Medaka
with. Default 120.
--quality_score QUALITY_SCORE
The quality score cutoff for isONclust. Default 7.