title: Sam2bam: High-Performance Framework for NGS Data Preprocessing Tools.
abstract: This paper introduces a high-throughput software tool framework called sam2bam that enables users to significantly speed up pre-processing for next-generation sequencing data. The sam2bam is especially efficient on single-node multi-core large-memory systems. It can reduce the runtime of data pre-processing in marking duplicate reads on a single node system by 156-186x compared with de facto standard tools. The sam2bam consists of parallel software components that can fully utilize multiple processors, available memory, high-bandwidth storage, and hardware compression accelerators, if available. The sam2bam provides file format conversion between well-known genome file formats, from SAM to BAM, as a basic feature. Additional features such as analyzing, filtering, and converting input data are provided by using plug-in tools, e.g., duplicate marking, which can be attached to sam2bam at runtime. We demonstrated that sam2bam could significantly reduce the runtime of next generation sequencing (NGS) data pre-processing from about two hours to about one minute for a whole-exome data set on a 16-core single-node system using up to 130 GB of memory. The sam2bam could reduce the runtime of NGS data pre-processing from about 20 hours to about nine minutes for a whole-genome sequencing data set on the same system using up to 711 GB of memory.
authors.affiliation: IBM Research-Tokyo, Tokyo, Japan.
authors.forename: Takeshi
authors.identifier: http://orcid.org/0000-0002-4021-5239
authors.initials: T
authors.lastname: Ogasawara
authors.affiliation: IBM Systems, Austin, TX, United States of America.
authors.forename: Yinhe
authors.initials: Y
authors.lastname: Cheng
authors.affiliation: IBM Systems, Poughkeepsie, NY, United States of America.
authors.forename: Tzy-Hwa Kathy
authors.initials: TK
authors.lastname: Tzeng
mesh_terms: D019295:Computational Biology / Q000379:methods; D059472:Exome; D016678:Genome; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software