SeQuiLa

SeQuiLa computes depth of coverage from next-generation sequencing (NGS) data to support analyses such as RNA-sequencing, copy number variant detection, and sequencing quality control.

Key Features:

• Depth of coverage computation: Performs depth of coverage calculations for NGS data as a core function.
• Scalability and performance: Reports over 100 times speedup compared to existing state-of-the-art tools for coverage computation.
• Big data technologies: Built on big data technologies to enable large-scale data processing.
• Structured Query Language API: Exposes a Structured Query Language (SQL) API for expressing coverage computations.
• SeQuiLa platform integration: Implemented as an extension to the SeQuiLa platform.
• Exome and genome support: Supports exome- and genome-wide coverage calculations.
• Distributed computing: Operates on distributed computing clusters and local environments for parallelized processing.
• NGS preprocessing optimization: Targets the computationally demanding preprocessing step of depth of coverage within NGS workflows.

Scientific Applications:

• RNA-sequencing analysis: Enables coverage-based analyses in RNA-sequencing workflows.
• Copy number variant detection: Supports coverage calculations used for copy number variant (CNV) detection.
• Sequencing quality control: Provides coverage metrics for sequencing quality control procedures.
• Exome and genome analyses: Facilitates exome- and genome-wide coverage assessments for genomic studies.

Methodology:

Implemented as an extension to the SeQuiLa platform using big data technologies and a Structured Query Language (SQL) API to perform distributed depth of coverage calculations on NGS data.