IonCRAM: a reference-based compression tool for ion torrent sequence files

 IonCRAM: a reference-based compression tool for ion torrent sequence files https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7487613/ 

 IonCRAM, the first reference-based compression tool to compress Ion Torrent BAM files for long term archiving. For the BAM files, IonCRAM could achieve a space saving of about 43%. This space saving is superior to what achieved with the CRAM format by about 8–9%.

Future research for reducing the space consumption of the Ion Torrent BAM files would include the binning of the flow signal and quality values. The idea of binning was initially introduced by Illumina [27] to reduce the space consumption of the quality values. This initiative was immediately followed by intensive research to optimize the binning procedure and address its effect on the downstream analysis, especially on the variant calling step [28–31]. We think that the binning of flow signals and quality data of Ion Torrent would also be successful, provided that the manufacturer contribute to this research. We added an option to IonCRAM for binning the flow signals, in a similar way to the binning method implemented in [26], and measured its effect on compression (Supplementary File 1). We left the step for investigating the effect of this binning on the downstream analysis to further research.

It is worth mentioning that IonCRAM has not been only used for the test data in the paper, it has also been used to compress and backup thousands of files for the Saudi Human Genome Program. IonCRAM is an open source and it is available for free along with the related test data at the tool website http://ioncram.saudigenomeproject.com.