######## Nerea 16S dataset - ASV generation, taxonomic assignment  #########

## Files in the current project:

# -AUGMENTED OBSERVATORY NEREA-16S DATA (2019-2020)	Table derived from 16_ASV_table.tsv (output of  4. 16S_export.sh) and 16_ASV_table_taxonomy.tsv (output of 6. 16S_export.s) by also converting sample IDs using 
# (continued)						NEREA samples codes according to SampleID_table_conversion.tsv
# -SampleID_table_conversion.tsv			Table to convert 16S fastq sequences published in the ENA project PRJEB74641 into NEREA samples IDs
# -1. 16S_import.sh					bash script to import paired-end sequence data into QIIME2 for quality analysis and initial processing
# -2. 16S_trim.sh					bash script to trim primers and adapters from raw sequence data using QIIME2
# -3. 16S_denoise.sh					bash script to perform denoising of sequence data using DADA2 via QIIME2 to construct ASV tables
# -4. 16S_export.sh					bash script to export ASV count tables and representative sequences from QIIME2 for further analysis
# -5a/b/c. 16S_taxonomy.sh				bash scripts to classify ASVs using different reference databases and methods.
# -6. 16S_export.sh					bash script to export refined ASV tables and sequences after further processing
# -16S_manifest_file.csv				Manifest file for importing raw sequence data into QIIME2.
# -16S_statistics and intermediate files.zip		Zip file including: 
									-16S_denoised_rep-seqs-dada2.qzv: Contains the representative sequences obtained after denoising with the DADA2 algorithm.
									-16S_denoised_stats-dada2.qzv: Provides statistical summaries and quality metrics of the denoised sequences processed by DADA2.
									-16S_denoised_summary.qzv: Offers a general summary of the denoised 16S sequences, possibly including read counts and sequence length distributions.
									-16S_denoised_table.qzv: Includes a feature table showing the abundance of denoised sequences across different samples.
									-16S_raw.qzv: Likely represents the raw 16S sequence data before any processing or denoising.
									-16S_table_taxonomy.qzv: Contains taxonomic classification information for the sequences, linking sequence features to their corresponding taxa.
									-16S_trim.qzv: Shows the trimmed sequences, possibly after removing low-quality bases and adapters before further processing.