NGS Sequencing

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Genome assembly:

Our bioinformatics department is offering several standard bioinformatics services, including NGS data preprocessing, Genome assembly, Genome annotation and Comparative genome analysis. Our team is also offering custom-tailored analyses.

We provide both De-novo and reference genome assembly for many small genomes such as plant, bacterial, bacteriophage, virus, and some fungal genomes. We use the software applications such as SPAdes, Abyss, and Velvet for the draft assembly of short reads. However, draft assemblies usually results in many gapped scaffold sequences. To remedy this, we apply automated strategies called SSPACE and GapFiller. These are reliable tools capable of closing gaps within scaffolds, using paired-reads. These methods show good results for both bacterial and eukaryotic datasets.

Delivered output:

  • Raw data quality reports;
  • Assembly summary report, containing results from genome assembly and quality statistics;
  • Generated contigs and scaffolds in Fasta format;
  • Bandage output files, visualizing de novo assembly graphs.

Genome annotation:

Genome annotation follows Genome assembly and describes individual genes and their products – RNA or proteins. We offer structural and functional genome annotation, encompassing the prediction of open reading frames (ORFs), gene structure (exon-intron structure), regulatory motifs, as well as assigning biological functions to these elements. This process involves both manual and automated annotation. We perform a search in multiple prominent databases such as KEGG, Uni-Prot/Swiss-Prot, GeneOnthology, etc. In addition, our service includes the widely used homology-searching programs BLAST and BLAST2Go, along with several Web-based annotating platforms such as DOGMA, Web Apollo, GenSAS, and RAST.

Delivered output:

  • Annotated genes in GFF and GeneBank formats;
  • Reports, containing a full annotation of coding sequence regions, tRNA and rRNA.