NGS Bioinformatics Pipelines

Advanced Data Analysis for Next Generation Sequencing (NGS) projects will excellerate your research and shorten your time to publication. A data quality check is already included in our standard NGS project, but we also offer more extensive analysis to visualize and interprete your FASTQ data. We provide comprehensive packages of different bioinformatics pipelines additionally to our NGS services. Examples of our validated pipelines are described below.

 

 

Variant Calling  

   

Variant Calling
The variant calling or SNP Discovery pipeline is an excellent addition to resequencing and exome sequencing projects. We perform several quality control and filter steps to provide you with the best reliable data. The SNP quality is assessed and variants are reported in VCF (variant call format) and spreadsheet formats. This specific pipeline is an ideal start for a custom genotyping project to design your custom SNP-array. Download the SNP Discovery Guideline now.

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 RNA Seq

mRNA Seq Expression Analysis
Not every organism studied in research is available as an off the shelf micorarray product. Besides that, the costs of sequencing are reducing drastically and can compete with the gene expression profiling on microarrays. We have a standard workflow available for the analysis for any organism. We can therefore offer an all-in service: from sample prep, sequencing using the HiSeq 2500 or the NextSeq 500, to differential expression analysis. Download the RNA Seq Analysis Guideline now.

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 miRNA sequencing

   

miRNA and small RNA Sequencing
Regulation of expression analysis can be contributed to microRNAs. We have developed a validated pipeline for the detection, quantification, and differential expression analysis of small non-coding RNA molecules.

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 Microbial genome sequencing

Automated Assembly and Annotation (prokaryotes)
Use our de novo assembly and annotation pipeline for assembling prokaryotic genomes using short-read data from our Illumina sequencers which can be combined with long-read data generated from for example the PacBio RS II sequencer. Gene finding with the assembled contigs or genome is performed, followed by annotation using publicly available data sources such as Genbank, KEGG, etc.

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Xenograft Analysis
Are you using human cell lines in a mouse model? Or studying plant-microbe or plant-fungal interactions at molecular level? We offer you the option of sequencing mixed organism samples, and performing an in silico separation of the sequence data, after which we analyze one or both different datasets.

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Interested in one of the above bioinformatic packages? Or are you looking for a tailor-made sequencing analysis solution? Contact us for free consultancy and information on our NGS and bioinformatics services.