The fastq/SAM/BAM format includes the NGS reads and related quality scores. The BAM file is the binary version of the readable SAM text file. (The read is the sequence of a DNA fragment). The output of this step is a sequence file composed of a set of reads in the fastq format as in Illumina technology or in the unaligned BAM format as in Ion Torrent technology. Therefore, efficient data compression should be implemented to reduce the storage footprint, which in turn reduces the cost of the test.įor medical applications, the NGS analytical pipeline starts with the step of base calling, where the physical signals (either images or electrical signals) are translated to sequences of nucleotide bases. For either option, the cost of data storage is part of the total cost for provisioning the service per sample. This requirement necessitates that the NGS lab possesses a high capacity storage systems either in site or in the cloud. Accreditation entities, such as the College of American Pathologists, require that the NGS laboratory maintains the data (as it is) for at least two years (2017 CAP Regulation MOL.35870, revised ). The Ion Torrent technology is not favored for whole genome sequencing due to its limited throughput, which would lead to insufficient depth for clinical use.įor clinical labs, the NGS data should be retained for a certain period of time. Whole exome sequencing covers the whole set of genes and is mostly used to identify novel mutations and genes. Gene panels are used to read the sequences of selected genes to screen for variations related to some inherited disorders and cancer. It is basically used for clinical gene panels and whole exome sequencing. This technology is particularly popular in the medical domain, because it is fast and cost effective. Ion Torrent is one of the widely used Next Generation Sequencing (NGS) technologies, with a market share of 20% (Research and Market Report 2016). The Creative Commons Public Domain Dedication waiver ( ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made.
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