{
    "comment": "this is the default config for nanopore single cell long read data using 10x 3'end kit. use splice annotation in alignment. ",
    "pipeline_parameters": {
        "seed": 2022,
        "threads": 8,
        "demultiplexer": "BLAZE",
        "do_barcode_demultiplex": true,
        "do_gene_quantification": true,
        "do_genome_alignment": true,
        "do_isoform_identification": true,
        "bambu_isoform_identification": false,
        "multithread_isoform_identification": false,
        "do_read_realignment": true,
        "do_transcript_quantification": true,
        "oarfish_quantification": true
    },
    "additional_arguments": {
        "oarfish": [],
        "BLAZE": [
            "--10x-kit-version",
            "3v3"
        ]
    },
    "barcode_parameters": {
        "max_bc_editdistance": 2,
        "max_flank_editdistance": 8,
        "segments": [
            {
                "type": "FIXED",
                "pattern": "CTACACGACGCTCTTCCGATCT",
                "name": "primer"
            },
            {
                "type": "MATCHED",
                "pattern": "NNNNNNNNNNNNNNNN",
                "name": "CB",
                "bc_list_name": "CB",
                "group": "",
                "buffer_size": 5,
                "max_edit_distance": 2
            },
            {
                "type": "RANDOM",
                "pattern": "NNNNNNNNNNNN",
                "name": "UB"
            },
            {
                "type": "FIXED",
                "pattern": "TTTTTTTTT",
                "name": "polyT"
            }
        ],
        "barcode_groups": [],
        "strand": "-",
        "TSO_seq": "AAGCAGTGGTATCAACGCAGAGTACATGGG",
        "TSO_prime": 5,
        "cutadapt_minimum_length": 10,
        "full_length_only": false
    },
    "isoform_parameters": {
        "generate_raw_isoform": false,
        "max_dist": 10,
        "max_ts_dist": 100,
        "max_splice_match_dist": 10,
        "min_fl_exon_len": 40,
        "max_site_per_splice": 3,
        "min_sup_cnt": 5,
        "min_cnt_pct": 0.001,
        "min_sup_pct": 0.2,
        "bambu_ndr": 0.5,
        "bambu_verbose": false,
        "bambu_trust_reference": true,
        "strand_specific": 0,
        "remove_incomp_reads": 4,
        "downsample_ratio": 1
    },
    "alignment_parameters": {
        "use_junctions": true,
        "no_flank": false
    },
    "realign_parameters": {
        "use_annotation": true
    },
    "transcript_counting": {
        "min_tr_coverage": 0.4,
        "min_read_coverage": 0.4
    }
}
