instance_seed: 1
negative:
    - '001'
    - '002'
    - '003'
calibration:
    - '001'
    - '002'
    - '003'
    - '004'
evaluation:
    - '001'
    - '002'
    - '003'
    - '004'
host_ratio: 0.849
prok_ratio: 0.15
vir_ratio: 0
euk_ratio: 0.001
targets:
    - prok
contaminants:
    - euk
targets_taxonomy: ncbi
contaminants_taxonomy: ncbi
sd_lognormal_vir: 1
sd_lognormal_euk: 2
sd_lognormal_prok: 2
prok_nb: 100
euk_nb: 20
vir_nb: 0
unknown_organisms_ratio: 0
core_simul: 0
sampling_date_limit: 2022/01/01
prok_taxa:
     - Actinobaculum sp. oral taxon 183
     - Actinomyces dentalis
     - Actinomyces gerencseriae
     - Actinomyces israelii
     - Actinomyces johnsonii
     - Actinomyces massiliensis
     - Actinomyces naeslundii
     - Actinomyces sp. oral taxon 170
     - Actinomyces sp. oral taxon 175
     - Actinomyces sp. oral taxon 180
     - Actinomyces sp. oral taxon 414
     - Actinomyces sp. oral taxon 448
     - Actinomyces sp. oral taxon 849
     - Actinomyces sp. oral taxon 877
     - Actinomyces sp. oral taxon 897
     - Schaalia meyeri
     - Schaalia odontolytica
     - Corynebacterium matruchotii
     - Rothia aeria
     - Rothia dentocariosa
     - Arachnia propionica
     - Arachnia rubra
     - Olsenella sp. oral taxon 807
     - Bacteroidetes oral taxon 274
     - Porphyromonas catoniae
     - Porphyromonas endodontalis
     - Porphyromonas sp. oral taxon 278
     - Porphyromonas sp. oral taxon 279
     - Alloprevotella rava
     - Alloprevotella sp. oral taxon 473
     - Alloprevotella tannerae
     - Prevotella baroniae
     - Prevotella denticola
     - Prevotella jejuni
     - Prevotella loescheii
     - Prevotella maculosa
     - Prevotella marshii
     - Prevotella melaninogenica
     - Prevotella micans
     - Prevotella multiformis
     - Prevotella nigrescens
     - Prevotella oralis
     - Prevotella oris
     - Prevotella oulorum
     - Prevotella pallens
     - Prevotella saccharolytica
     - Prevotella salivae
     - Prevotella shahii
     - Prevotella sp. oral taxon 306
     - Prevotella sp. oral taxon 313
     - Prevotella sp. oral taxon 317
     - Prevotella sp. oral taxon 472
     - Prevotella sp. oral taxon 820
     - Prevotella veroralis
     - Tannerella forsythia
     - Tannerella serpentiformis
     - Tannerella sp. oral taxon 808
     - Capnocytophaga gingivalis
     - Capnocytophaga granulosa
     - Capnocytophaga ochracea
     - Capnocytophaga sp. oral taxon 323
     - Capnocytophaga sp. oral taxon 326
     - Capnocytophaga sp. oral taxon 329
     - Capnocytophaga sp. oral taxon 332
     - Capnocytophaga sp. oral taxon 336
     - Capnocytophaga sp. oral taxon 338
     - Capnocytophaga sp. oral taxon 380
     - Capnocytophaga sp. oral taxon 412
     - Capnocytophaga sp. oral taxon 864
     - Capnocytophaga sp. oral taxon 902
     - Capnocytophaga sputigena
     - Candidatus Saccharibacteria bacterium oral taxon 488
     - Gemella haemolysans
     - Gemella morbillorum
     - Streptococcus anginosus
     - Streptococcus constellatus
     - Streptococcus gordonii
     - Streptococcus intermedius
     - Streptococcus mitis
     - Streptococcus oralis
     - Streptococcus sp. F0441
     - Streptococcus sp. oral taxon 071
     - Eubacterium brachy
     - Eubacterium infirmum
     - Eubacterium saphenum
     - Mogibacterium diversum
     - Mogibacterium timidum
     - Lachnospiraceae bacterium oral taxon 096
     - Catonella morbi
     - Lachnoanaerobaculum saburreum
     - Oribacterium sp. oral taxon 078
     - Stomatobaculum longum
     - Filifactor alocis
     - Peptostreptococcus stomatis
     - Solobacterium moorei
     - Centipeda periodontii
     - Selenomonas artemidis
     - Selenomonas flueggei
     - Selenomonas infelix
     - Selenomonas noxia
     - Selenomonas sp. oral taxon 126
     - Selenomonas sp. oral taxon 136
     - Selenomonas sp. oral taxon 137
     - Selenomonas sp. oral taxon 138
     - Selenomonas sp. oral taxon 892
     - Selenomonas sp. oral taxon 920
     - Selenomonas sputigena
     - Anaeroglobus geminatus
     - Dialister invisus
     - Dialister pneumosintes
     - Megasphaera micronuciformis
     - Veillonella atypica
     - Veillonella dispar
     - Veillonella parvula
     - Parvimonas micra
     - Fusobacterium hwasookii
     - Fusobacterium massiliense
     - Fusobacterium nucleatum
     - Fusobacterium periodonticum
     - Fusobacterium sp. CM1
     - Fusobacterium sp. CM22
     - Fusobacterium sp. HMSC064B11
     - Fusobacterium sp. oral taxon 203
     - Leptotrichia buccalis
     - Leptotrichia hofstadii
     - Leptotrichia shahii
     - Leptotrichia sp. oral taxon 212
     - Leptotrichia sp. oral taxon 215
     - Leptotrichia sp. oral taxon 218
     - Leptotrichia sp. oral taxon 225
     - Leptotrichia sp. oral taxon 417
     - Leptotrichia sp. oral taxon 498
     - Leptotrichia wadei
     - Eikenella corrodens
     - Kingella oralis
     - Neisseria flavescens
     - Neisseria sicca
     - Neisseria sp. oral taxon 014
     - Campylobacter concisus
     - Campylobacter gracilis
     - Campylobacter rectus
     - Campylobacter showae
     - Cardiobacterium hominis
     - Aggregatibacter aphrophilus
     - Aggregatibacter segnis
     - Aggregatibacter sp. oral taxon 458
     - Haemophilus parainfluenzae
     - Treponema denticola
     - Treponema lecithinolyticum
     - Treponema maltophilum
     - Treponema medium
     - Treponema pectinovorum
     - Treponema socranskii
     - Treponema vincentii
     - Fretibacterium fastidiosum
euk_taxa:
    - Ascomycota
    - Mucoromycota
vir_taxa: []
tech: 'HS25'
read_length: 150
total_reads_nb: 20000000
fragment_mean_size: 300
fragment_sd: 25
max_base_quality: 35
evaluation_taxlevel:
    - phylum
    - class
    - order 
    - family
    - genus
    - species
calibration_fdr: best_f1
calibration_function: median # mean/median/max threshold of all
use_prokncbi: 1
no_evaluation: []
rank_to_sort_by: species
filtering_threshold: 5
