Standardizing the next generation of bioinformatics software development with BioHDF (HDF5).
Next Generation Sequencing technologies are limited by the lack of standard bioinformatics infrastructures that can reduce data storage, increase data processing performance, and integrate diverse information. HDF technologies address these requirements and have a long history of use in data-intensive science communities. They include general data file formats, libraries, and tools for working with the data. Compared to emerging standards, such as the SAM/BAM formats, HDF5-based systems demonstrate significantly better scalability, can support multiple indexes, store multiple data types, and are self-describing. For these reasons, HDF5 and its BioHDF extension are well suited for implementing data models to support the next generation of bioinformatics applications.
Mason
Christopher E
CE
Geospiza Inc, Seattle, WA 98119, USA.
Zumbo
Paul
P
Sanders
Stephan
S
Folk
Mike
M
Robinson
Dana
D
Aydt
Ruth
R
Gollery
Martin
M
Welsh
Mark
M
Olson
N Eric
NE
Smith
Todd M
TM
D019295:Computational Biology; D003198:Computer Simulation; D003628:Database Management Systems; D030541:Databases, Genetic; D016415:Sequence Alignment / Q000592:standards / Q000706:statistics & numerical data* / Q000639:trends; D017421:Sequence Analysis / Q000592:standards / Q000706:statistics & numerical data* / Q000639:trends; D012984:Software / Q000592:standards / Q000639:trends; D012985:Software Design; D014584:User-Computer Interface