Bioinformatics_ohmx
Nanopore-seq bioinformatics
Nanopore-seq bioinformatics
A standard nanopore bioinformatics package includes:
  • Basecalling.
  • Read and barcode preprocessing.
  • A full QC report of the sequencing run.
  • Alignment to a reference genome (e.g. human hg38).
  • Files which allow visualization on a genome browser.
Advanced nanopore bioinformatics depend on the application:

Clinical diagnostics:

 

  • Genotyping of a full ROI (including SNVs and structural variations).
  • Consensus sequence determination.
  • Diagnostic pipeline development.

 

Epigenetic analysis:

 

  • Genotyping of a full ROI (including SNVs and structural variations).
  • Consensus sequence determination.
  • Diagnostic pipeline development.

 

Microbiome analysis:

 

  • Metagenomic/metatranscriptomic classification to identify microbial genera, species or pathogens.
  • Specific analysis of informative genes (full 16S and 23S rRNA).
  • Metagenomic assembly.

 

Other applications:

 

  • Quantitative analysis and differential expression/isoform analysis.
  • Genomic assembly.
  • Clone validation.
  • Development of custom pipelines and tools.