Next Generation Sequencing Data

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Unlock the full value of your next-generation sequencing (NGS) data sets from Illumina HiSeq/MiSeq/NextSeq/HiSeq X Ten, Roche 454 GS-FLX, LifeTechnologies Solid and Iontorrent /IonProton PGM, and PacBio platforms.

Bespoke NGS data analysis: QFAB provides tailored bioinformatics services to biologists across the spectrum of computational techniques and services applicable to molecular biology and next generation sequencing. QFAB researchers design and implement custom bioinformatics approaches that are developed in consultation with researchers for specific questions in molecular biology.

We can also integrate your genomics data with other –omics, microarrays and clinical datasets.

Our NGS data analysis services include:

Whole genome sequencing data analysis

  • Assembly and mapping
  • Structural and functional annotation of the genome (ORF detection, assignment of genes,…)
  • Samples comparison
  • Expertise in human whole genome sequencing data analysis and gene variant analysis. QFAB is also a partner of the Garvan Institute of Medical Research for human whole genome sequencing using the Illumina HiSeq X Ten platform
  • Expertise in plant de novo genome assembly
  • PacBio bacterial genomes assembly


Automate your NGS data analysis with a custom analysis workflow. We can design and develop your pipelines, run them on our infrastructure,  in the cloud or deploy it on your own systems.


  • De novo transcriptome assembly
  • Differential expression analysis
  • Detailed statistical analysis
  • Detection of novel splice isoforms or transcripts

Also available:

  • Alternative splicing
  • Calling for SNP variants
  • Pathway analysis
  • Time series analysis
  • Visualisation in genome browser

Annotation pipeline

  • Prediction of coding regions
  • Annotation of coding genes, non-coding RNA, tRNA, rRNA, miRNA…
  • Repeat identification
  • Statistics of annotation and analysis of GC content

ChipSeq Data Analysis

  • Mapping and genes identification
  • Comparison if samples regulated by the same transcription factor
  • Peak identification and reporting of genomic regions differing between control and experimental samples
  • Preparation of Wiggle track formatted files containing peak profile data for each of the ChIP-Seq sequence libraries (hosting for display in UCSC Genome Browser available)
  • Statistics

Also available: methylation data analysis

Exome Data Analysis

  • Listing of identified mutations between the studies samples and the reference: SNPs, InDels
  • Identification of known mutations by comparing the results to international databases
  • Influence of the mutation on the protein functionality

Also available: methylation data analysis

Amplicon sequence mapping or assembly/ Mutation and variant detection

  • Mutation and variant detection (SNP, CNV, InDels)
  • Identification and positioning of known and unknown mutations
  • Transcription: Influence of the mutation on the protein functionality


16 survey or microbial community WGS

  • Creation of reference database and alignment for organisms identification
  • Adjustments of interpretation settings
  • Taxonomic trees
  • Samples comparison
  • Comparative metagenomics