jkimlab/rbrc repository overview

⁠OVERVIEW

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

⁠INSTALLATION

docker pull jkimlab/rbrc

⁠RUNNING RBRC

1. Prepare reference directory with all reference sequence files and read directory with all paired-end fastq files.

2. Make output directory.

3. Prepare params.txt file as follows into the output directory

     #---------------------------------------------------------------------------------------#
    ## Mendatory !
    # Reference genomes
    REF	1	<Reference name 1> /rbrc_wd/reference/<reference_sequence1.fa>
    REF	2	<Reference name 2> /rbrc_wd/reference/<reference_sequence2.fa>
   
    # NGS reads
    # FASTQ
    >LIB1
    /rbrc_wd/read/<F read fastq file>
    /rbrc_wd/read/<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>
    #---------------------------------------------------------------------------------------#
   

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4. Run RBRC with follow command

   docker run -v /LOCALDISK/reference:/rbrc_wd/reference -v /LOCALDISK/read:/rbrc_wd/read -v /LOCALDISK/output:rbrc_wd/output -t rbrc:latest RBRC.pl -p /rbrc_wd/output/params.txt -o /rbrc_wd/output
   

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⁠RBRC output

1. 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
            
   

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2. Assembly output

    output_directory/SPAdes/Final_assembly/assembly.fasta
   

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