High tail hall 2 full torrent9/6/2023 ![]() Two commonly used NGS platforms, Illumina and Ion Torrent, recommend maximum fragment lengths of about 300 and 400 nucleotides, respectively ( 2). Another challenge when amplifying target genes with well-established universal primer pairs is related to fragment size optimization. When analyzing the sequence diversity of 10 genes in 100 samples, barcoding with fusion primers would require 1000 barcoded primers (10 genes × 100 samples), making the task both laborious and expensive without dual indexing, which is only available on the Illumina MiSeq platform. Barcodes can be added to the PCR amplicons either by ligation or by performing the PCR amplification with fusion primers, which include both the barcodes and sequencing adapters. The efficiency of next-generation sequencing (NGS) of PCR amplicons has increased via sample barcoding ( 1), which facilitates multiplex sequencing of numerous samples and genes (such as ribosomal RNA or protein-coding genes) in the same run.
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