params.json

{
    "input": "/workspace/assemblyqc/testdata/v2/assemblysheet.csv",
    "outdir": "./results",
    "email": null,
    "check_sequence_duplicates": true,
    "assemblathon_stats_n_limit": 100,
    "gfastats_skip": false,
    "ncbi_fcs_adaptor_skip": false,
    "ncbi_fcs_adaptor_empire": "euk",
    "ncbi_fcs_gx_skip": false,
    "ncbi_fcs_gx_tax_id": 3750,
    "ncbi_fcs_gx_db_path": "/workspace/ComparativeDataSources/NCBI/FCS/GX/r2023-01-24",
    "contamination_stops_pipeline": false,
    "tidk_skip": false,
    "tidk_repeat_seq": "TTTAGGG",
    "tidk_filter_by_size": true,
    "tidk_filter_size_bp": 1000000,
    "busco_skip": false,
    "busco_mode": "genome",
    "busco_lineage_datasets": "embryophyta_odb10 eudicots_odb10",
    "busco_download_path": "/workspace/ComparativeDataSources/BUSCO/assemblyqc",
    "lai_skip": false,
    "kraken2_skip": false,
    "kraken2_db_path": "/workspace/ComparativeDataSources/kraken2db/k2_pluspfp_20240904",
    "hic": null,
    "hic_skip_fastp": false,
    "hic_skip_fastqc": false,
    "hic_fastp_ext_args": "--qualified_quality_phred 20 --length_required 50",
    "hic_samtools_ext_args": "-F 3852",
    "merqury_skip": false,
    "merqury_kmer_length": 21,
    "synteny_skip": false,
    "synteny_mummer_skip": false,
    "synteny_plotsr_skip": false,
    "synteny_xref_assemblies": "/workspace/assemblyqc/testdata/v2/xrefsheet.csv",
    "synteny_between_input_assemblies": true,
    "synteny_mummer_plot_type": "both",
    "synteny_mummer_m2m_align": false,
    "synteny_mummer_max_gap": 1000000,
    "synteny_mummer_min_bundle_size": 1000000,
    "synteny_plot_1_vs_all": false,
    "synteny_color_by_contig": true,
    "synteny_plotsr_seq_label": "Chr",
    "synteny_plotsr_assembly_order": "gddh13_v1p1 m9_v1 m9_v1_h1 m9_v1_h2",
    "orthofinder_skip": false
}