SOMLIT-Astan metabarcoding time-series datasets

In the frame of the French coastal environment observation network SOMLIT (physicochemical parameters), a plankton monitoring is performed at the SOMLIT-Astan site (western English Channel, 2.5 nautical miles off Roscoff, Brittany, France, 60 m depth - 48°46′18′′ N–3°58′6′′ W). Plankton samples were collected bi-monthly during high neap tide at 1 m depth using a 5L Niskin bottle). DNA was extracted and metabarcoding sequenced for size-fractionated samples (0.2–3 µm and >3 µm) from 2009 to 2016. The 18S V4 marker was sequenced for the entire period, while 18S V1V2, COI, petB, and SSU [18S + 16S] V4V5 markers were sequenced only from 2009 to 2012. Raw sequencing data are available for download at EBI-ENA (PRJEB96022).
The archive somlit_astan_metab_v1.1.0.zip contains datasets for all five markers, including for each marker:
- ASV sequences in FASTA format (somlit-astan_{marker}_ampliseq.fasta.gz)
- Read count per bioinformatic step (somlit-astan_{marker}_ampliseq_log.tsv)
- A MULTIQC report (somlit-astan_{marker}_ampliseq_multiqc.html)
- A nf-core/ampliseq report detailing each bioinformatic step (somlit-astan_{marker}_ampliseq_report.html)
- ASV table with taxonomy and counts (somlit-astan_{marker}_ampliseq_table.tsv.gz)
- Code archive with bash scripts launching the nextflow workflow nf-core/ampliseq and R scripts formatting the outputs (somlit-astan_{marker}-ampliseq-v1.1.0.zip)
- A README (HTML) detailing file contents and parameters (somlit-astan_{marker}_README.html)