Bioinformatic analysis of NGS data

Modern sequencing technologies now produce millions of high-quality reads per run, generating a vast amount of data that poses a significant challenge for many researchers.

The Bioinformatics Service at CEINGE offers advanced expertise in the analysis of data derived from high-throughput sequencing (NGS). The primary goal is to support research groups in extracting maximum value from their sequencing experiments by providing customized data analysis strategies and specialized consultancy.

EQUIPMENT

5 Linux servers, each with 128 GB of RAM and 32 cores
Over 100 TB of disk space for temporary data storage
Over 200 TB of disk space for long-term data storage

This infrastructure, combined with up-to-date software and advanced scripting expertise, optimizes data analysis workflows and ensures rapid result delivery

SERVICES

1. DNA-seq Analysis (targeted, exome, and whole genome sequencing)

In silico gene panel design
Sequence quality control
De novo genome assembly
Sequence alignment against reference genomes
Variant calling, annotation, and prioritization (single samples, matched normal-tumor pairs, family trios)
Internal software for variant interpretation (VAReVAL)
Gene ontology and pathway enrichment analysis
CNV and large genomic rearrangement analysis
Study of clonal evolution and tumor heterogeneity

2. Metagenomics Analysis

16S RNA sequencing
Identification of microbial community composition

3. RNA-seq Analysis

Sequence quality control
De novo transcriptome assembly
Differential expression analysis of genes, isoforms, and exons
Identification of fusion genes, circular RNAs, and trans-splicing events
Detection of long non-coding RNAs (lncRNAs)
Gene ontology and pathway enrichment analysis
Gene expression-dependent survival analysis

4. Epigenetic Analysis

ChIP-Seq data analysis (transcription factors, histones)
Bisulfite sequencing data analysis (Methyl-Seq)
Differential methylation analysis in CpG and non-CpG regions
Hi-C data analysis

Service Access and Options

The facility offers two levels of service for the analyses described above:

1. Standard Solution

Delivery of raw analysis results (e.g., list of annotated variants, differentially expressed genes with statistical data, binding sites, etc.).
No additional interpretation or in-depth discussion of the experiment by the service.
Pricing based on a standard cost per sample, in addition to sequencing costs.