Biocarriers Inocc. 3
wastewater metagenome
R3 Biofilm reactor d0
biochem_oxygen_dem
2000 mg/l
chem_oxygen_dem
2000 mg/l
collection_date
2021-06-09
description
R3 Biofilm reactor d0
env_biome
sewage
env_feature
urine material
env_material
bioreactor
geo_loc_name
Switzerland: Zurich
lat_lon
47.4039 N 8.6102 E
nitrate
25 mg N/l
organism
wastewater metagenome
ph
7.5
primary_treatment
alkalinization
rel_to_oxygen
microaerophilic
samp_store_loc
freezer
samp_store_temp
-20
samp_vol_we_dna_ext
1.5 mL
sample_title
Biocarriers Inocc. 3
secondary_treatment
Partial nitritation/ anammox
seq_methods
"Clipping of adapter and primer sequences was done using cutadapt (v4.1). Reads with ambiguous base-calls (Ns) were first removed to accurately map short adapter and primer sequences. Paired-end reads without an exact match to the forward and reverse adapter and primer sequence were removed. Further processing of the sequencing data was done with the DADA2 R package (v1.24.0) in R (v 4.2.2) according to (Callahan et al. 2016). As first quality control step, truncation was done with a quality score cut-off (truncQ=2). Additional filtering to eliminate reads containing any ambiguous base calls or reads with high expected errors (maxEE=2,2) was performed. Reads mapping to the Phix genome were discarded as well. After dereplication, further denoising using the Divisive Amplicon Denoising Algorithm (DADA) error estimation algorithm and the sample inference algorithm selfConsist (with nbases=1e8) was done. The obtained error rates were checked and monotonicity was enforced in the model fit to deal with binned quality scores. The loess function was reweighted (log10 transformation of total transition probabilities) whilst the span was adjusted to 2. Denoised reads inferred were subsequently merged. Finally, the amplicon sequence variant (ASV) table obtained after the removal of chimera was used for taxonomy assignment. This was done with the Naive Bayesian Classifier (with an 80% minimal bootstrap confidence threshold) and the DADA2 formatted Silva v132 and RDP trainset 16 reference taxonomy according to (Quast et al. 2013; Wang et al. 2007). "
sewage_type
municipal
sludge_retent_time
200+ days
soluble_inorg_mat
ammonia 50 mg N/L
wastewater_type
urine
BioSampleModel
MIMARKS.survey.wastewater.4.0