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 tool is open source and available at Code Ocean, github, and. The space saving achieved by our tool is a practical step in this direction. Therefore, developing efficient compression software for clinical NGS data goes beyond the computational interest as it ultimately contributes to the overall cost reduction of the clinical test. Reducing the space consumption of NGS data reduces the cost of storage and data transfer. This space saving is superior to what achieved with the CRAM format by about 8–9%. For the BAM files, IonCRAM could achieve a space saving of about 43%.

In this paper, we present IonCRAM, the first reference-based compression tool to compress Ion Torrent BAM files for long term archiving. This missing feature has motivated us to develop a new program to improve the compression of the Ion Torrent files for long term archiving. However, the tools for generating the CRAM formats are not designed to handle the flow signals. Compressing SAM/BAM into CRAM format significantly reduces the space needed to store the NGS results. The flow signals occupy a big portion of the BAM file (about 75% for the human genome). In addition to the usual SAM/BAM fields, the Ion Torrent BAM file includes technology-specific flow signal data. The built-in software for the Ion Torrent sequencing machines delivers the sequencing results in the BAM format. Ion Torrent is one of the major next generation sequencing (NGS) technologies and it is frequently used in medical research and diagnosis.

Ultra Model Set 1 Torrent