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

ABSTRACT:

Background

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

SUBMITTER: Shokrof M 

PROVIDER: S-EPMC7487613 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature