Marijn11
External Id
SAMN38813426
External Id
mothur
INSDC center name
2023-12-13T00:00:00Z
INSDC first public
2023-12-14T12:19:19.710Z
INSDC last update
SRS19858892
INSDC secondary accession
live
INSDC status
MIMARKS.survey.wastewater.4.0
NCBI submission model
MIMARKS.survey.wastewater.6.0
NCBI submission package
SRS19858892
SRA accession
2000 mg/l
biochem_oxygen_dem
2000 mg/l
chem_oxygen_dem
2021-08-04
collection_date
R3 Ref reactor d55
description
R3 Ref reactor d55
description
sewage
env_biome
urine material
env_feature
bioreactor
env_material
Switzerland: Zurich
geo_loc_name
47.4039 N 8.6102 E
lat_lon
25 mg N/l
nitrate
wastewater metagenome
http://purl.obolibrary.org/obo/NCBITaxon_527639
organism
wastewater metagenome
organism
7.5
ph
alkalinization
primary_treatment
microaerophilic
rel_to_oxygen
freezer
samp_store_loc
-20
samp_store_temp
1.5 mL
samp_vol_we_dna_ext
suspended Sludge Inocc. 3
sample_title
Partial nitritation/ anammox
secondary_treatment
"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). "
seq_methods
municipal
sewage_type
200+ days
sludge_retent_time
ammonia 50 mg N/L
soluble_inorg_mat
suspended Sludge Inocc. 3
title
urine
wastewater_type