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Table 5 Comparison of the most commonly used high-throughput sequencing platforms for characterizing the soil microbiomes.

From: Soil microbiota manipulation and its role in suppressing soil-borne plant pathogens in organic farming systems under the light of microbiome-assisted strategies

PlatformaGenerationSequencing technologyRead lengthOutput/runError
rate
Example of useType of instrument and run timeTaxonomic resolution level
IlluminaSecond generationSequencing by synthesisShort reads
1 × 36 bp − 2 × 300 bp
0.3–1000 GbLowVariant callingBenchtop
2–29 h
Low-resolution
Ion TorrentThird generationSequencing by synthesisShort reads
200–400 bp
0.6–15 GbLowVariant callingBenchtop
2–4 h
Low-resolution
PacBioFourth generationSingle molecule sequencing by synthesisLong reads
up to 60 kb
0.5–10 GbHighDe novo assembly of small bacterial genomes and large genome finishingLarge scale
0.5–4 h
High-resolution
Oxford NanoporeFourth generationSingle moleculeLong reads
up to 100 kb
0.1–20 GbHighComplete genome of isolates and metagenomicsPortable
1 min–48 h
High-resolution
  1. aRoche 454-pyrosequencing (First-generation platform) is discontinued from 2016
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