Table 1.

Usual terms utilized in most NGS techniques.

Term	Definition
α-diversity	Measures the diversity associated with a single sample (e.g. OTU number, Shannon Index, rarefaction curve, etc.)
Assembly	Partial reconstruction of genes or genomes by aligning and merging short sequencing reads
Barcodes	Short nucleotides sequences merged with primers and/or adaptors allowing simultaneous sequencing of DNA from multiple samples and further separation in silico
β-diversity	Measures the diversity among samples (e.g. heatmaps, venn diagrams, similarity trees, PCAs, ordinations etc.)
Binning	Separation of all fragments originating from a common taxon or OTU
Contig	Set of small overlapping DNA segments representing a consensus region of DNA
Coverage	Means how deep was the sequencing effort in sampling a given community; number of times a nucleotide is read during sequencing
Denoising	Quality processing applied to 16S rDNA reads, correcting the “noise” (errors) artificially generated during sequencing
Diversity estimators	e.i. Shannon – Estimate the diversity, taking into account the number of species and how even they are distributed
OTU	Operational taxonomic unit. A cluster of sequences within a given similarity cut-off (e.g. 3%, which is usually utilized to define bacterial species by 16S rDNA)
Sequencing trimming	Processing of sequencing reads, which includes the removal of primers and barcodes, deletion of a given sequence region and elimination of low quality and very short reads
Phylogenetic assignment	Assignment of each sequence or OTU to its known closest relative organism
Rarefaction curve	Curve representing the richness of the sample according to the number of sequences. The shape of the curve reflects the sample diversity
Richness estimators	OTU, Ace, Chao1 - Estimate the number of species (or genus, orders etc.) in a given sample by different methods