These are the second set of data files to be submitted to (Eur)OBIS: taxonomic occurrences from the COI, 18S, and ITS marker gene omics data, sampling event metadata, and image metadata for the events of ARMS-MBON's second sampling campaign (all ARMS deployed in 2020 and 2021 and retrieved between and 2020 and 2022). This includes:
- The three 18S files: DNA extension, EMOF, Occurrence extension (processed dates: April 2021, Aug. 2023, Sept 2020)
- The three CO1 files: DNA extension, EMOF, Occurrence extension (processed dates: April 2021, Aug. 2023, Sept 2020)
- The three ITS files: DNA extension, EMOF, Occurrence extension (processed dates: April 2021, Sept. 2020)
- The observatory data and a metadata file explaining the entries therein; sampling event data (and its metadata file), omics data (and its metadata file). These are subset of the entire ARMS-MBON data set that can be found in combined event data
- Additionally, a file with metadata about the images obtained during the sampling events and of the ARMS plates. These are subset of the entire ARMS-MBON data set that can be found in combined event data. Images are currently stored in PlutoF and can be downloaded by accessing the links in the "Download URL" column.
The source files for the omics and taxonomic data can be found in the analysis_release_002 repository: the input and output files for the bioinformatics analysis done with PEMA can be found there. Links to the PEMA pipeline can also be found there. The code that was used to reforumlate PEMA outputs and search various databases for associated information can be found in code_release_002.
Contaminants have been filtered out with decontam (R) using run-specific negative controls and the prevalence method. ASVs flagged as contaminants were removed prior to data release. Detailed scripts are provided in code_release_002.
For more information on ARMS-MBON, see its data landing page and references there in.
Note that these files in the combined data folder may also be useful to you:
- A list of the ENA project, sample, and run accession numbers for all the ARMS-MBON data to date
- A list of the area/field and sample/technical replicates for all the ARMS-MBON data to date
- Additional sequencing demultiplexing metadata - see the README in the folder for an explanation; the subset of those samples relevant to this data release can be found on demultiplexing_details_OmicsData_release002.csv.