NGS applications and data analysis

NGS technologies enable sequencing in a high throughput manner with low cost generating significant amounts of data. Nowadays, NGS data analysis is the bottleneck of these technologies. This has arisen the need for new paradigms in data computation and knowledge extraction. That is the reason why we have specialized in dealing with new computational and bioinformatic challenges.

To achieve the best results, we always offer a personalized advice, both in scientific and technical procedures.

Quality control of NGS raw data, before they are used for deeper analysis downstream, is mandatory in all data analysis.

READ ABOUT THE ANALYSIS WE OFFER BELOW

DNAseq

The availability of NGS platforms, has significantly increased the scale of many DNA-sequencing (DNAseq) applications.

Additionally, we provide help with obtaining high‐quality samples, deciding the number of replicates to use, the best library preparation, sequencing platform and coverage value. For more information, see the Experimental design section.

De novo genome assembly.

De novo assembly is a method for constructing genomes from a large number of (short- or long-) DNA fragments, with no a priori knowledge of the correct sequence or order of those fragments. The first step is the alignment of reads with each other to reconstruct the original DNA sequence computationally, which ideally generates continuous regions of DNA.

Use cases

- If there is no reference genome.
- When the technology offers advantages over the reference-guided one.
- Detect variants (especially structural) that cannot be determined using the reference genome.

Genome resequencing

Resequencing the genome of individuals for which there is a reference genome allows investigation of the relationship between sequence variation and normal or disease phenotypes.

Use cases

- Obtain single nucleotide polymorphisms (SNPs) and insertions- deletions (indels).
- Indicate large rearrangements (e.g., translocations, inversions, large copy number variations).
- Identify functional genes and markers of important traits.
- Genomic map construction.
- Population genetics research.

Target resequencing of specific regions

In this application, a subset of regions of the genome or genes are sequenced. It focuses on the data analysis of specific areas of interest.

Use cases

Targeted analysis can include the sequencing of:

- The exome (protein-coding region of genes in a genome).
- Specific genes of interest.
- Informative loci for diseases or taxonomic classification.
- Intergene regions.
- Mitochondrial DNA.

Variant calling and annotation

This application is usually linked to genome/targeted region resequencing although sometimes is also used after de novo assembly. Adequate for the identification and characterization of structural (e.g. copy number variation, inversions, translocations, mobile elements) and non-structural variations (SNPs, MNPs, indels).

Use cases

- Genotyping (germline mutations).
- Identify rare SNPs within a population.
- Identify somatic mutations.
- Detect somatic SNVs within an individual using multiple tissue samples.
- Discover copy number variation (CNV) and other structural variants.
- Variant comparison between samples and recurrent variant extraction.
- Variant annotation with databases and predictive algorithms.

RNAseq

RNAseq data analysis

RNA sequencing (RNAseq) uses NGS to reveal the presence and quantity of RNA in a biological sample at a given time, analysing the continuously changing cellular transcriptome.

Use cases

- Identify the full catalogue of transcripts or discover new ones.
- Search for isoforms and gene fusion events.
- Analyse the differential expression of genes, isoforms and exons and perform functional analysis afterwards.
- Assemble a de novo transcriptome for downstream analysis.

Metagenomics

Metagenomic analysis enable the characterization and quantification of the microbial communities present in a sample. The metagenomic analysis has improved in the last years due to the increase throughput, decrease in cost of sequencing data and technological advances.

Amplicon-based metagenomics

This application is used for the study of a region of interest through amplicons, generated by PCR. Targeted amplicons analysis of various ribosomal RNA coding DNA (16S, 18S rDNA) and other conserved markers (such as ITS for fungi) is useful for taxonomic classification.

Use cases

- Quantify the taxonomic diversity of a metagenomic sample.
- Discover the diversity of species in a sample (alpha diversity) or the diversity in microbial community between different environments or samples (beta diversity).
- Predict metabolic and biological pathways.
- Examine hundreds of samples in order to evaluate differential analysis and taxonomy diversity classification.

Shotgun metagenomics

Besides being able to perform the same type of analysis as amplicon-based metagenomics application, shotgun metagenomics enables full genome sequencing of all the organisms present in the sample for downstream analysis.

Use cases

- Identify rare or novel organisms in the community that are otherwise difficult or impossible to analyse.
- Assemble total or partial genomes present in the sample.
- Discover the presence or absence of functional pathways in samples.
- Predict and annotate genes.

CHIP-seq

ChIP-seq data analysis

ChIP-sequencing is a method used to analyse protein-DNA interactions. These interactions can strongly influence the regulation of gene expression and are critical for understanding how the cell is operating. The experiment requires, as a first step, cross-linking of chromatin to stabilize the interaction between protein factors and chromatin and identify the binding sites of DNA-associated proteins.

Use cases

- Profile histone methylation through the genome to detect epigenetic events
- Discover the nucleosomes position and density.
- Detect transcription factor binding sites.

Other applications

If you have any other request, please contact us.