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config.yaml
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config.yaml
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#mandatory, one of them or both
sra_samples: example_sra_samples.tsv
local_samples: example_local_samples.tsv
#assembly
minimum_quality_base: 28
minimum_read_length: 50
sliding_window_size: 5
sliding_window_quality_threshold: 20
adapter_file_name: NexteraPE-PE.fa
adapter_removal_param1: 3
adapter_removal_param2: 25
adapter_removal_param3: 6
cov_cutoff: 5
spades_kmer_sizes: 21,33,55,77,99,111,127
#resistance and typing
species: Mycobacterium_tuberculosis
#typing
minimum_coverage_for_calling: 10
minimum_alternate_fraction_for_calling: 0.75
snp_threshold: 0
minimum_spanning_tree_size: 10
phylogeny_image_size: 800
#virulence
virulence_factors: virulence_factors.tsv
virulence_percentage_identity_cutoff: 80
virulence_coverage_cutoff: 70
# reference for snp calling:
# 1. cgMLST
# 2. one or multiple samples listed in local_samples/sra_samples (assembled genomes)
# 3. one genome from NCBI using assembly UID (eg: 33148 for S. aureus COL genome, see page https://www.ncbi.nlm.nih.gov/assembly/GCF_000012045.1/)
# 4. combination of options 1-3 (comma separated list, no spaces: "cgMLST,ecoli39,33148")
reference: "cgMLST"
# snp calling method: either "freebayes_joint_genotyping" or "gatk_gvcfs"
snp_caller: "gatk_gvcfs"
# mapping: either bwa or bwa_stringent
mapping: "bwa"
# /data/databases/amplicon_based_metagenomics/16S/ezbiocloud201805/QIIME/DB_amp_vsearch_format.fasta
16S_database: /data/databases/amplicon_based_metagenomics/16S/ezbiocloud201805/QIIME/DB_amp_vsearch_format.fasta