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config.json
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config.json
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{
"meta" : {
"authors": ["Camille Scott", "Weiming Li", "Titus Brown"],
"description": "",
"data_type": ["RNA-seq", "DNA-seq"],
"date": 2015
},
"pipeline": {
"prefix": "petMarSB",
"work_dir": "_work",
"trimmomatic": {
"params": "LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:32",
"n_threads": 1
},
"blast": {
"evalue": 0.000001,
"params": "",
"threads": 4
},
"bowtie2_build": {
"n_threads": 4,
"extra_args": "--offrate 1"
},
"bowtie2_align": {
"n_threads": 4,
"extra_args": "--mm -a -X 600 --rdg 6,5 --rfg 6,5 --score-min L,-.6,-.4 --no-discordant --no-mixed"
},
"busco": {
"path": "/work/BUSCO_v1.1b1/BUSCO_v1.1b1.py",
"n_threads": 4,
"vert_url": "http://busco.ezlab.org/files/vertebrata_buscos.tar.gz",
"metazoa_url": "http://busco.ezlab.org/files/metazoa_buscos.tar.gz",
"db_dir": "busco_db",
"output_suffix": "busco.results"
},
"hmmscan": {
"n_threads": 8
},
"cmscan": {
"n_threads": 8,
"db_dir": "cm_db"
},
"khmer": {
"normalize": {
"single": {
"ksize": 25,
"table_size": 2e9,
"n_tables": 4,
"coverage": 20
},
"pooled": {
"ksize": 25,
"table_size": 8e9,
"n_tables": 4,
"coverage": 20
}
},
"filter-abund": {
"coverage": 20,
"min_abund": 2
}
},
"transdecoder": {
"n_threads": 8,
"min_prot_len": 80,
"orf_cutoff": 600
}
}
}