PartitionedAssembly/partitioned_assembly.json at master · ChaissonLab/PartitionedAssembly · GitHub

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{
    "bam" : ["/home/cmb-16/nobackups/mjc/sample_datasets/hgsvg/HG00514/UMD_Sequel_II/pbmm2/HG00514.PacBioSequel2.EDEVI_20190319_S64018_PL100119428-5_B01.subreads.bam.sorted.bam", "/home/cmb-16/nobackups/mjc/sample_datasets/hgsvg/HG00514/UMD_Sequel_II/pbmm2/HG00514.PacBioSequel2.EDEVI_20190321_S64018_PL100119428-5_B01.subreads.bam.sorted.bam"],
    "working_dir" : "/home/cmb-panasas2/mchaisso/HG00514_2_flye",
    "sample" : "HG00514",
    "ref" : "/home/cmb-16/mjc/shared/references/hg38_noalts/indexes/lra/hg38.no_alts.fasta",
    "vcf" : "/home/cmb-16/mjc/projects/hgsvg/analysis/HG00514/Phasing/SH032.wgs.whatshap.strandseq-10X.20160704.phased-genotypes.vcf.gz",
		"grid_large" : "sbatch --time=24:00:00 --partition=cmb",
		"grid_manycore" : "sbatch --time=48:00:00 --partition=cmb",
		"grid_medium" : "sbatch --time=24:00:00 --partition=cmb",
		"grid_small" : "sbatch --time=4:00:00 --partition=cmb",
		"grid_blat" : "sbatch --time=24:00:00 --partition=cmb",
    "read-type" : "raw",
    "consensus" : "arrow",
    "assembler" : "flye"
}