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config.sample.json
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config.sample.json
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{
"project" : "B2R-Maike",
"pandaseq_overlap": "10",
"pandaseq_quality": "25",
"pandaseq_minlength": "100",
"pandaseq_maxlength": "700",
"forward_primer": "CCTACGGGNGGCWGCAG",
"reverse_primer": "GACTACHVGGGTATCTAATCC",
"silva_release" : "123",
"silva_db" : "/data/db/mothur/silva_nr119/silva.nr_v119.align",
"silva_arb": "/data/db/Silva/128/SSURef_NR99_128_SILVA_07_09_16_opt.arb",
"sina_version": "1.3.0-r24042",
"sina_min_sim" : "0.95",
"basedir": "../data/",
"metadata": "../data/metadata.csv",
"data": {
"cult1A-1": { "forward":"../data/DMP01935_L1_cult1A.1.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult1A.1.raw_2.fq.gz"},
"cult1A-2": { "forward":"../data/DMP01935_L1_cult1A.2.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult1A.2.raw_2.fq.gz"},
"cult1A-3": { "forward":"../data/DMP01935_L1_cult1A.3.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult1A.3.raw_2.fq.gz"},
"cult1A-4": { "forward":"../data/DMP01935_L1_cult1A.4.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult1A.4.raw_2.fq.gz"},
"cult1A-5": { "forward":"../data/DMP01935_L1_cult1A.5.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult1A.5.raw_2.fq.gz"},
"cult1F-1": { "forward":"../data/DMP01935_L1_cult1F.1.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult1F.1.raw_2.fq.gz"},
"cult1F-2": { "forward":"../data/DMP01935_L1_cult1F.2.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult1F.2.raw_2.fq.gz"},
"cult1F-3": { "forward":"../data/DMP01935_L1_cult1F.3.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult1F.3.raw_2.fq.gz"},
"cult1F-4": { "forward":"../data/DMP01935_L1_cult1F.4.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult1F.4.raw_2.fq.gz"},
"cult1F-5": { "forward":"../data/DMP01935_L1_cult1F.5.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult1F.5.raw_2.fq.gz"},
"cult2A-1": { "forward":"../data/DMP01935_L1_cult2A.1.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult2A.1.raw_2.fq.gz"},
"cult2A-2": { "forward":"../data/DMP01935_L1_cult2A.2.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult2A.2.raw_2.fq.gz"},
"cult2A-3": { "forward":"../data/DMP01935_L1_cult2A.3.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult2A.3.raw_2.fq.gz"},
"cult2A-4": { "forward":"../data/DMP01935_L1_cult2A.4.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult2A.4.raw_2.fq.gz"},
"cult2A-5": { "forward":"../data/DMP01935_L1_cult2A.5.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult2A.5.raw_2.fq.gz"},
"cult2F-1": { "forward":"../data/DMP01935_L1_cult2F.1.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult2F.1.raw_2.fq.gz"},
"cult2F-2": { "forward":"../data/DMP01935_L1_cult2F.2.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult2F.2.raw_2.fq.gz"},
"cult2F-3": { "forward":"../data/DMP01935_L1_cult2F.3.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult2F.3.raw_2.fq.gz"},
"cult2F-4": { "forward":"../data/DMP01935_L1_cult2F.4.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult2F.4.raw_2.fq.gz"},
"cult2F-5": { "forward":"../data/DMP01935_L1_cult2F.5.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult2F.5.raw_2.fq.gz"},
"cult3A-1": { "forward":"../data/DMP01935_L1_cult3A.1.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult3A.1.raw_2.fq.gz"},
"cult3A-2": { "forward":"../data/DMP01935_L1_cult3A.2.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult3A.2.raw_2.fq.gz"},
"cult3A-3": { "forward":"../data/DMP01935_L1_cult3A.3.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult3A.3.raw_2.fq.gz"},
"cult3A-4": { "forward":"../data/DMP01935_L1_cult3A.4.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult3A.4.raw_2.fq.gz"},
"cult3A-5": { "forward":"../data/DMP01935_L1_cult3A.5.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult3A.5.raw_2.fq.gz"},
"cult3F-1": { "forward":"../data/DMP01935_L1_cult3F.1.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult3F.1.raw_2.fq.gz"},
"cult3F-2": { "forward":"../data/DMP01935_L1_cult3F.2.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult3F.2.raw_2.fq.gz"},
"cult3F-3": { "forward":"../data/DMP01935_L1_cult3F.3.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult3F.3.raw_2.fq.gz"},
"cult3F-4": { "forward":"../data/DMP01935_L1_cult3F.4.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult3F.4.raw_2.fq.gz"},
"cult3F-5": { "forward":"../data/DMP01935_L1_cult3F.5.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult3F.5.raw_2.fq.gz"},
"cult4A-1": { "forward":"../data/DMP01936_L1_cult4A.1.raw_1.fq.gz", "reverse":"../data/DMP01936_L1_cult4A.1.raw_2.fq.gz"},
"cult4A-2": { "forward":"../data/DMP01936_L1_cult4A.2.raw_1.fq.gz", "reverse":"../data/DMP01936_L1_cult4A.2.raw_2.fq.gz"},
"cult4A-3": { "forward":"../data/DMP01936_L1_cult4A.3.raw_1.fq.gz", "reverse":"../data/DMP01936_L1_cult4A.3.raw_2.fq.gz"},
"cult4A-4": { "forward":"../data/DMP01936_L1_cult4A.4.raw_1.fq.gz", "reverse":"../data/DMP01936_L1_cult4A.4.raw_2.fq.gz"},
"cult4A-5": { "forward":"../data/DMP01936_L1_cult4A.5.raw_1.fq.gz", "reverse":"../data/DMP01936_L1_cult4A.5.raw_2.fq.gz"},
"cult4F-1": { "forward":"../data/DMP01936_L1_cult4F.1.raw_1.fq.gz", "reverse":"../data/DMP01936_L1_cult4F.1.raw_2.fq.gz"},
"cult4F-2": { "forward":"../data/DMP01936_L1_cult4F.2.raw_1.fq.gz", "reverse":"../data/DMP01936_L1_cult4F.2.raw_2.fq.gz"},
"cult4F-3": { "forward":"../data/DMP01936_L1_cult4F.3.raw_1.fq.gz", "reverse":"../data/DMP01936_L1_cult4F.3.raw_2.fq.gz"},
"cult4F-4": { "forward":"../data/DMP01935_L1_cult4F.4.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult4F.4.raw_2.fq.gz"},
"cult4F-5": { "forward":"../data/DMP01935_L1_cult4F.5.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult4F.5.raw_2.fq.gz"},
"cult5A-1": { "forward":"../data/DMP01935_L1_cult5A.1.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult5A.1.raw_2.fq.gz"},
"cult5A-2": { "forward":"../data/DMP01935_L1_cult5A.2.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult5A.2.raw_2.fq.gz"},
"cult5A-3": { "forward":"../data/DMP01935_L1_cult5A.3.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult5A.3.raw_2.fq.gz"},
"cult5A-4": { "forward":"../data/DMP01935_L1_cult5A.4.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult5A.4.raw_2.fq.gz"},
"cult5A-5": { "forward":"../data/DMP01935_L1_cult5A.5.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult5A.5.raw_2.fq.gz"},
"cult5F-1": { "forward":"../data/DMP01935_L1_cult5F.1.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult5F.1.raw_2.fq.gz"},
"cult5F-2": { "forward":"../data/DMP01935_L1_cult5F.2.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult5F.2.raw_2.fq.gz"},
"cult5F-3": { "forward":"../data/DMP01935_L1_cult5F.3.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult5F.3.raw_2.fq.gz"},
"cult5F-4": { "forward":"../data/DMP01935_L1_cult5F.4.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult5F.4.raw_2.fq.gz"},
"cult5F-5": { "forward":"../data/DMP01935_L1_cult5F.5.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult5F.5.raw_2.fq.gz"},
"cult6A-1": { "forward":"../data/DMP01935_L1_cult6A.1.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult6A.1.raw_2.fq.gz"},
"cult6A-2": { "forward":"../data/DMP01935_L1_cult6A.2.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult6A.2.raw_2.fq.gz"},
"cult6A-3": { "forward":"../data/DMP01935_L1_cult6A.3.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult6A.3.raw_2.fq.gz"},
"cult6A-4": { "forward":"../data/DMP01935_L1_cult6A.4.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult6A.4.raw_2.fq.gz"},
"cult6A-5": { "forward":"../data/DMP01935_L1_cult6A.5.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult6A.5.raw_2.fq.gz"},
"cult6F-1": { "forward":"../data/DMP01935_L1_cult6F.1.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult6F.1.raw_2.fq.gz"},
"cult6F-2": { "forward":"../data/DMP01935_L1_cult6F.2.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult6F.2.raw_2.fq.gz"},
"cult6F-3": { "forward":"../data/DMP01935_L1_cult6F.3.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult6F.3.raw_2.fq.gz"},
"cult6F-4": { "forward":"../data/DMP01935_L1_cult6F.4.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_cult6F.4.raw_2.fq.gz"},
"soilA-1": { "forward":"../data/DMP01935_L1_soilA.1.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_soilA.1.raw_2.fq.gz"},
"soilA-2": { "forward":"../data/DMP01935_L1_soilA.2.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_soilA.2.raw_2.fq.gz"},
"soilA-3": { "forward":"../data/DMP01935_L1_soilA.3.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_soilA.3.raw_2.fq.gz"},
"soilA-4": { "forward":"../data/DMP01935_L1_soilA.4.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_soilA.4.raw_2.fq.gz"},
"soilF-1": { "forward":"../data/DMP01935_L1_soilF.1.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_soilF.1.raw_2.fq.gz"},
"soilF-2": { "forward":"../data/DMP01935_L1_soilF.2.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_soilF.2.raw_2.fq.gz"},
"soilF-3": { "forward":"../data/DMP01935_L1_soilF.3.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_soilF.3.raw_2.fq.gz"},
"soilF-4": { "forward":"../data/DMP01935_L1_soilF.4.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_soilF.4.raw_2.fq.gz"},
"wild1A-1": { "forward":"../data/DMP01935_L1_wild1A.1.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild1A.1.raw_2.fq.gz"},
"wild1A-2": { "forward":"../data/DMP01935_L1_wild1A.2.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild1A.2.raw_2.fq.gz"},
"wild1A-3": { "forward":"../data/DMP01935_L1_wild1A.3.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild1A.3.raw_2.fq.gz"},
"wild1A-4": { "forward":"../data/DMP01935_L1_wild1A.4.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild1A.4.raw_2.fq.gz"},
"wild1A-5": { "forward":"../data/DMP01935_L1_wild1A.5.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild1A.5.raw_2.fq.gz"},
"wild1F-1": { "forward":"../data/DMP01935_L1_wild1F.1.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild1F.1.raw_2.fq.gz"},
"wild1F-2": { "forward":"../data/DMP01935_L1_wild1F.2.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild1F.2.raw_2.fq.gz"},
"wild1F-3": { "forward":"../data/DMP01935_L1_wild1F.3.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild1F.3.raw_2.fq.gz"},
"wild1F-4": { "forward":"../data/DMP01935_L1_wild1F.4.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild1F.4.raw_2.fq.gz"},
"wild1F-5": { "forward":"../data/DMP01935_L1_wild1F.5.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild1F.5.raw_2.fq.gz"},
"wild2A-1": { "forward":"../data/DMP01935_L1_wild2A.1.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild2A.1.raw_2.fq.gz"},
"wild2A-2": { "forward":"../data/DMP01935_L1_wild2A.2.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild2A.2.raw_2.fq.gz"},
"wild2A-3": { "forward":"../data/DMP01935_L1_wild2A.3.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild2A.3.raw_2.fq.gz"},
"wild2A-4": { "forward":"../data/DMP01935_L1_wild2A.4.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild2A.4.raw_2.fq.gz"},
"wild2A-5": { "forward":"../data/DMP01935_L1_wild2A.5.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild2A.5.raw_2.fq.gz"},
"wild2F-1": { "forward":"../data/DMP01935_L1_wild2F.1.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild2F.1.raw_2.fq.gz"},
"wild2F-2": { "forward":"../data/DMP01935_L1_wild2F.2.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild2F.2.raw_2.fq.gz"},
"wild2F-3": { "forward":"../data/DMP01935_L1_wild2F.3.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild2F.3.raw_2.fq.gz"},
"wild2F-4": { "forward":"../data/DMP01935_L1_wild2F.4.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild2F.4.raw_2.fq.gz"},
"wild2F-5": { "forward":"../data/DMP01935_L1_wild2F.5.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild2F.5.raw_2.fq.gz"},
"wild3A-1": { "forward":"../data/DMP01935_L1_wild3A.1.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild3A.1.raw_2.fq.gz"},
"wild3A-2": { "forward":"../data/DMP01935_L1_wild3A.2.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild3A.2.raw_2.fq.gz"},
"wild3A-3": { "forward":"../data/DMP01935_L1_wild3A.3.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild3A.3.raw_2.fq.gz"},
"wild3A-4": { "forward":"../data/DMP01935_L1_wild3A.4.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild3A.4.raw_2.fq.gz"},
"wild3A-5": { "forward":"../data/DMP01935_L1_wild3A.5.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild3A.5.raw_2.fq.gz"},
"wild3F-1": { "forward":"../data/DMP01935_L1_wild3F.1.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild3F.1.raw_2.fq.gz"},
"wild3F-2": { "forward":"../data/DMP01935_L1_wild3F.2.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild3F.2.raw_2.fq.gz"},
"wild3F-3": { "forward":"../data/DMP01935_L1_wild3F.3.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild3F.3.raw_2.fq.gz"},
"wild3F-4": { "forward":"../data/DMP01935_L1_wild3F.4.raw_1.fq.gz", "reverse":"../data/DMP01935_L1_wild3F.4.raw_2.fq.gz"}
},
"adapters_fasta": "/data/ngs/adapters/contaminant_list.txt"
}