Second generation
- Illumina MiSeq: maximum sequence length capacity 2x300bp, total output up to 15GigaBase. Ideal for short amplicons or re-sequencing analyses.
- Illumina NextSeq500: maximum sequence length capacity 2×150, total output up to 120GigaBase. Ideal for short amplicons or re-sequencing analyses.
- Illumina NextSeq2000 (new): maximum sequence length capacity 2×300, total output up to 360GigaBase. Ideal for (meta)genomic and (meta)transcriptomic analyses, short amplicons or for re-sequencing analyses.
Third generation
- Oxford Nanopore MinIon: maximum capacity for long sequences (up to 100Kb), total output up to 30GigaBase. Ideal for genomic/metagenomic analyses where portability or speed in obtaining results is an important factor.
- PacBio Sequel II (new): capacity for ~4,000,000 HiFi sequences with a length of ~10Kb (Circular Consensus Sequences, CCS), and with a quality of ~Q80. Ideal for complete genomes in search of resistance factors, virulence or new genomic characteristics or fo long amplicons sequencing such as the microbial 16S ribosomal gene, reaching a depth of taxonomic annotation down to the species or strain level.