ReadDB provides efficient storage for mapped short reads.

ABSTRACT:

Background

The advent of high-throughput sequencing has enabled sequencing based measurements of cellular function, with an individual measurement potentially consisting of more than 108 reads. While tools are available for aligning sets of reads to genomes and interpreting the results, fewer tools have been developed to address the storage and retrieval requirements of large collections of aligned datasets. We present ReadDB, a network accessible column store database system for aligned high-throughput read datasets.

Results

ReadDB stores collections of aligned read positions and provides a client interface to support visualization and analysis. ReadDB is implemented as a network server that responds to queries on genomic intervals in an experiment with either the set of co

SUBMITTER: Rolfe PA 

PROVIDER: S-EPMC3143109 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature