Extraction_Blanks_1_2_3_Combined_DNA_Fish
metagenome
env_broad_scale
marine coastal environment
env_local_scale
lab
depth
NA
host
negative control
isolation_source
water_control
collection_date
2022-05-05
geo_loc_name
New Zealand: Cawthron Institue, Nelson
lat_lon
41.27 S 173.29 E
ref_biomaterial
negative control
samp_collect_device
Blank
samp_mat_process
extraction, PCR, metabarcoding
samp_size
0.001 L
Filtering_method
Blank
Filter_preservation_method
Blank
Sound
Blank
Gene_marker
16S_fish
Environmental_Nucleic_Acid
DNA
Sampling_Station
Blank
replicate
Extraction_1.2.3
Bioinformatics Applied
Cuadapt was used to remove primer sequences, allowing a single mismatch. Trimmed sequences then underwent processing with the 'DADA2' package in R. Reads were truncated 160 and 160 bp for the forward and reverse reads, respectively and filtered with a default maximum number of “expected errors” (maxEE), reads not meeting this threshold were discarded. A parametric error matrix was constructed, and sequence variants for the forward and reverse reads were dereplicated. Singletons were discarded, and paired-end reads were merged with no mismatch and a minimum overlap of 10 bp. Finally, chimeric sequences were eliminated using the consensus option in the removeBimeraDenovo function.
BioSampleModel
Metagenome or environmental