Table 5 Comparison of the most commonly used high-throughput sequencing platforms for characterizing the soil microbiomes.
Platforma | Generation | Sequencing technology | Read length | Output/run | Error rate | Example of use | Type of instrument and run time | Taxonomic resolution level |
|---|---|---|---|---|---|---|---|---|
Illumina | Second generation | Sequencing by synthesis | Short reads 1 × 36 bp − 2 × 300 bp | 0.3–1000 Gb | Low | Variant calling | Benchtop 2–29 h | Low-resolution |
Ion Torrent | Third generation | Sequencing by synthesis | Short reads 200–400 bp | 0.6–15 Gb | Low | Variant calling | Benchtop 2–4 h | Low-resolution |
PacBio | Fourth generation | Single molecule sequencing by synthesis | Long reads up to 60 kb | 0.5–10 Gb | High | De novo assembly of small bacterial genomes and large genome finishing | Large scale 0.5–4 h | High-resolution |
Oxford Nanopore | Fourth generation | Single molecule | Long reads up to 100 kb | 0.1–20 Gb | High | Complete genome of isolates and metagenomics | Portable 1 min–48 h | High-resolution |