CSI NGS Portal

CSI NGS Portal automates analysis of next-generation sequencing (NGS) data to perform genome alignment, expression quantification, and experiment-specific workflows for DNA, RNA, smallRNA, ChIP, RIP, 4C, SHAPE, circRNA, eCLIP, and Bisulfite sequencing.

Key Features:

• Automated Data Analysis: Integrates established bioinformatics pipelines to process NGS datasets and execute analysis workflows.
• Supported NGS Experiment Types: Provides analysis workflows for DNA, RNA, smallRNA, ChIP, RIP, 4C, SHAPE, circRNA, eCLIP, and Bisulfite sequencing.
• Input Format Support: Accepts raw sequencing data in FASTQ format for downstream processing.
• Comprehensive Pipeline Options: Implements 14 standard pipelines while supporting addition of new and customised pipelines.
• Genome Alignment and Quantification: Performs genome alignment and expression quantification as part of automated workflows.
• Result Interoperability: Produces ready-to-use outputs intended for further analysis or integration with other bioinformatics tools.
• Data Management: Utilises a MariaDB database on a Linux server for storage and result management.

Scientific Applications:

• Molecular Genetics: Enables analysis of genomic and transcriptomic data to investigate molecular genetics of cells in health and disease.
• Expression Profiling: Facilitates transcriptome and small RNA expression quantification across diverse experimental protocols.
• Epigenetics and Interactions: Supports analysis of ChIP, RIP, eCLIP, Bisulfite, and related assays to study protein–DNA/RNA interactions and DNA methylation.
• Structural and Conformation Studies: Supports 4C and SHAPE datasets for studies of chromatin conformation and RNA structure.

Methodology:

Accepts FASTQ uploads and runs established bioinformatics pipelines (14 standard pipelines with support for customised pipelines) to perform genome alignment and expression quantification for DNA, RNA, smallRNA, ChIP, RIP, 4C, SHAPE, circRNA, eCLIP, and Bisulfite sequencing, with results stored in a MariaDB database on a Linux server.