AssemblyAnalysis/assembly_analysis.json at master · ChaissonLab/AssemblyAnalysis · GitHub

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{
    "sample" : "HG00514",
    "sv-set": {"ins":"sample.SVset.ins.bed",
               "del":"sample.SVset.del.bed",
               "hap":"sample.SVset.hap.bed"
               },
    "bam": {"lra" : "/home/cmb-16/nobackups/mjc/sample_datasets/hgsvg/HG00514/UMD_Sequel_II/lra/HG00514.PacBioSequel2.EDEVI_20190319_S64018_PL100119428-5_B01.subreads.bam.sorted.lra.bam",
            "mm2": "/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"
            },
    "assemblies" : { "cov-30" : ["/home/cmb-16/mjc/mchaisso/projects/hgsvg/AssemblyAnalysis/HG00514.SequelII.CLR.30x.haplotype1.fa",
				 "/home/cmb-16/mjc/mchaisso/projects/hgsvg/AssemblyAnalysis/HG00514.SequelII.CLR.30x.haplotype2.fa",
                                 "CLR"]
                     "cov-40" : ["/home/cmb-16/mjc/mchaisso/projects/hgsvg/AssemblyAnalysis/HG00514.SequelII.CLR.40x.haplotype1.fa",
				 "/home/cmb-16/mjc/mchaisso/projects/hgsvg/AssemblyAnalysis/HG00514.SequelII.CLR.40x.haplotype2.fa",
                                 "CLR"]
		     "cov-50" : ["/home/cmb-16/mjc/mchaisso/projects/hgsvg/AssemblyAnalysis/HG00514.SequelII.CLR.50x.haplotype1.fa",
				 "/home/cmb-16/mjc/mchaisso/projects/hgsvg/AssemblyAnalysis/HG00514.SequelII.CLR.50x.haplotype2.fa",
                                 "CLR"]
		     "cov-75" : ["/home/cmb-16/mjc/mchaisso/projects/hgsvg/AssemblyAnalysis/HG00514.SequelII.CLR.75x.haplotype1.fa",
				 "/home/cmb-16/mjc/mchaisso/projects/hgsvg/AssemblyAnalysis/HG00514.SequelII.CLR.75x.haplotype2.fa",
                                 "CLR"]
		     "ctg-1": ["/home/cmb-16/mjc/mchaisso/projects/hgsvg/ChromPipeline/OneRun/assembly.1.consensus.fasta",
		               "/home/cmb-16/mjc/mchaisso/projects/hgsvg/ChromPipeline/OneRun/assembly.2.consensus.fasta",
                                 ""]
                     "ccs-1" : [ "/home/cmb-16/mjc/mchaisso/projects/hgsvg/ChromPipeline/CCS_2/assembly.1.consensus.fasta",
                                 "/home/cmb-16/mjc/mchaisso/projects/hgsvg/ChromPipeline/CCS_2/assembly.2.consensus.fasta",
                                 "CCS"]
                     "tworuns" : [ "/home/cmb-16/mjc/mchaisso/projects/hgsvg/ChromPipeline/TwoRuns/assembly.1.consensus.fasta",
                                   "/home/cmb-16/mjc/mchaisso/projects/hgsvg/ChromPipeline/TwoRuns/assembly.2.consensus.fasta",
                                 ""]
                     "flye2" : ["/home/cmb-panasas2/mchaisso/HG00514_2_flye/assembly.1.fasta",
                                "/home/cmb-panasas2/mchaisso/HG00514_2_flye/assembly.2.fasta",
                                 ""]
                     },
  "ref" : "/home/cmb-16/mjc/shared/references/hg38_noalts/indexes/lra/hg38.no_alts.fasta",

  "grid_large" : "sbatch -c 16 --mem=32G --time=24:00:00 --partition=cmb",
  "grid_medium" : "sbatch -c 2 --mem=16G --time=24:00:00 --partition=cmb",
  "grid_small" : "sbatch -c 1 --mem=6G --time=4:00:00 --partition=cmb",
  "grid_memory" : "sbatch -c 4 --mem=48G --time=24:00:00 --partition=cmb",

}