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Two review articles, have systematically surveyed these methods for PGM data and provided guidance concerning which tools to consider for benchmarking based on the data properties. These methods are classified into the following three categories: (1) suffix array/tree-based methods that use a suffix tree to detect and correct substitution and indel errors (e.g., Fiona ) (2) k-spectrum-based methods that divide reads into k-mer lengths and generate a k-mer depth profile to correct the k-mer profile (e.g., Blue and Pollux ) and (3) multiple sequence alignment (MSA)-based methods that use k-mers as seeds and construct a consensus sequence from the multiple alignments to correct errors (e.g., Coral and Karect ). These algorithms differ with respect to error models, statistical techniques, data features, the determined parameters, and performances. Several algorithms have been proposed to correct sequencing errors for PGM data (Table ). However, PGM has a relatively high insertion and deletion (indel) error rate of 1.5% (range from 0.46% to 2.4%). Ion Torrent Personal Genome Machine (PGM) technology is a mid-length read, low-cost and high-speed NGS platform with special applications in microbial sequencing. Next-generation sequencing (NGS) has been widely used in the study of viruses and has opened new avenues for research and diagnostic applications (e.g., viral mutant spectra, virus quasispecies theory and dynamics, fitness landscape, and discovery of novel viruses ). We found that the combined use of Pollux and Fiona gave the best results when error-correcting Ion Torrent PGM viral data. Of the algorithms tested, Pollux showed a better overall performance but tended to over-correct ‘genuine’ substitution variants, whereas Fiona proved to be better at distinguishing these variants from sequencing errors. Tests using both real and simulated data showed that the algorithms differed in their abilities to detect and correct errors and that the error rate and sequencing depth significantly affected the performance. Deletion errors were clearly present at the ends of homopolymer runs. We examined 19 quality-trimmed PGM datasets for the HBV reverse transcriptase (RT) region and found a total error rate of 0.48% ± 0.12%. A full systematic assessment of the effectiveness of various error correction algorithms in PGM viral datasets (e.g., hepatitis B virus (HBV)) has not been performed. Ion Torrent Personal Genome Machine (PGM) technology is a mid-length read, low-cost and high-speed next-generation sequencing platform with a relatively high insertion and deletion (indel) error rate. 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