Table 3.
List of currently available pipelines for meta-barcoding
| Name | Clustering algorithm | Yeast-specific | Ref. |
| Clotu | Identity-based clustering | Yes | [126] |
| PIPITS | Identity-based clustering | Yes | [116] |
| CloVR-ITS | Identity-based clustering | Yes | [127] |
| BioMaS | Reference-based | No | [129] |
| Kraken | Reference-based | No | [123] |
| Mothur | Mixed | No | [115] |
| Qiime (1 & 2) | Mixed | No | [119,124] |
| MICCA | Mixed | No | [128] |
| Vsearch | Identity-based | No | [117] |
| Uparse | Identity-based | No | [131] |
| Unoise (1 & 2) | Variant-based | No | [132] |
| DADA2 | Variant-based | No | [60] |
Clustering algorithms were divided into: (1) Identity-based, those relying on an empirical percentage of identity between two sequences for grouping them into a single cluster; (2) Reference-based, algorithms which group sequences into taxonomic bins according to their identities; (3) Variant-base, those defining sequence variants according to the presence of SNPs or mutations; (4) Mixed, pipelines which contain different algorithms for clustering.