Biomedical Engineering Reference
In-Depth Information
8
GenomicTools: an open source
platform for developing high-
throughput analytics in genomics
Aristotelis Tsirigos, Niina Haiminen,
Erhan Bilal and Filippo Utro
Abstract:
Following the dramatic reduction of sequencing cost,
research laboratories have been producing huge amounts of data,
measuring DNA variations, RNA abundances, protein-DNA
interactions, DNA methylation levels, and even chromosomal
conformations. Making sense of terabytes of data requires reliable
data management, computational resources, and, eventually,
effi cient computational methods for pre-processing, quality
control, analysis and meta-analysis. In this work, we present a
fl exible computational platform for facilitating the development of
pipelines to accomplish such computational tasks. For example, the
user can easily create average read profi les across transcriptional
start sites or enhancer sites, quickly prototype customized
peak discovery methods for ChIP-seq experiments, perform
genome-wide statistical tests such as enrichment analyses, and
design controls via user-designed randomization schemes, among
other applications.
Key words:
computational genomics; ChIP-seq; RNA-seq; BED
format; SAM format.
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