RBRC is a tool for NGS paired-end read clustering and de novo assembly based on Reference genome sequence-based read clustering

• gcc, g++ (7.5.0)
• make (GNU Make 4.1)
• java (1.8.0)
• wget (1.17.1)
• zip (3.0)
• git (2.7.4)

• Sort::Key::Natural (perl library)
• Bio::TreeIO (perl library)
• Parallel::ForkManager (perl library)
• Switch (perl library)

• Download and install using RBRC package from this github page. You can install all third party tools automatically for running RBRC using 'setup.pl'.

    git clone https://github.com/jkimlab/RBRC.git
    cd RBRC
    ./setup.pl --install
  

• If you use Docker, you can download and use RBRC with all dependencies through pulling docker image.

    docker pull jkimlab/rbrc
  

• If you want to see manual for running RBRC docker image, see 👉 RBRC Docker hub

    ./setup.pl --example
    bash example_cmd.sh

    * Before running this command, you have to set the examples of RBRC

• Options of running RBRC

    ./RBRC.pl -p [parameter file] -o [output directory]
  

• To run RBRC, you need to prepare a parameter file as follows

    #---------------------------------------------------------------------------------------#
    ## Mendatory !
    # Reference genomes
    REF	1	<Reference name 1> <Reference genome sequence 1>
    REF	2	<Reference name 2> <Reference genome sequence 2>
  
    # NGS reads
    # FASTQ
    >LIB1
    <F read fastq file>
    <R read fastq file>
  
    #---------------------------------------------------------------------------------------#
    ## Optional
    # Running paramters
    THREADS        <number of threads: default = 1>
    REF_SIMILARITY_CUTOFF <minimum cutoff value of properly mapped reads: default = 80>
    MAPQ <read mapping quality threshold: default = 0>
  
    # Pairwise alignment & synteny block construction params
    RESOLUTION	<Resolution to construct synteny: default = 10000
  
    # Physical coverage paramters
    PHY_CUTOFF	LIB1	<minimum cutoff value for physical coverage-based syntenic region break: default = 5>
  
    # Distance based clustering paramters
    DBC_READ_DIST_CUTOFF	<maximum cutoff value of read distance for matrix calculation: default = 1000>
  
    # Cluster merging parameter
    MERGE_MIN_READS	<minimum cutoff value of links to merge clusters: default = 5>
    #---------------------------------------------------------------------------------------#
  

• Clustering output

    output_directory/RBRC.cluster : list of cluster and clustered reads
     - Column 1: name of cluster
     - Column 2: Read ID
     
    [example]
            CLUSTER1	chr8-278460/1
            CLUSTER1	chr8-278460/2
            CLUSTER1	chr8-278414/1
            CLUSTER1	chr8-278414/2
            CLUSTER1	chr8-278396/1
            CLUSTER1	chr8-278396/2
            CLUSTER1	chr8-278392/1
            CLUSTER1	chr8-278392/2
            CLUSTER1	chr8-278382/1
            CLUSTER1	chr8-278382/2
  

• Assembly output

    output_directory/SPAdes/Final_assembly/assembly.fasta