Genome Assembly (reference-based)

Reference-based genome assembly reconstructs a genome by aligning sequencing reads against an existing reference genome from a closely related organism. This approach enables highly efficient and accurate genome reconstruction, making it ideal for identifying genetic variants, comparing strains or populations, and analysing well-characterised species. It is particularly valuable for clinical genomics, evolutionary studies, and large-scale genomic projects where speed, precision, and consistency are essential for generating reliable biological insights.

Base Pricing & Turnaround Time

Procaryote Genome

Rp. 300.000 ($ 20) per sample

7 days

Eucaryote Genome

Start from: Rp. 500.000 ($ 30) per sample

7 days

small-size genome (<150Mbp)

Eucaryote Genome

large-size genome (>150Mbp)

Start from: Rp. 1.000.000 ($ 60) per sample

7 days

MODEL ORGANISM

Eucaryote Genome

large-size genome (>150Mbp)

NON-MODEL ORGANISM

Start from: Rp. 1.500.000 ($ 90) per sample

Start from: 7 days

Default Deliverables

  • Assembled Genome
    FASTA format containing consensus genome sequences reconstructed through alignment against a reference genome, including mapped contigs or polished assemblies.

  • Assembly Metrics Report
    Comprehensive quality assessment, including read mapping rate, coverage depth, genome coverage percentage, GC content, consensus quality, and assembly completeness.

  • Annotation Files

    • GFF3/GTF: gene coordinates and structural features

    • CDS sequences (FNA): nucleotide coding regions

    • Protein sequences (FAA): translated gene products

  • Functional Annotation
    Functional characterisation of predicted genes, including Gene Ontology (GO), KEGG pathways, Pfam domains, InterPro annotations, and more.

  • Standard Variant Discovery
    Identification of genomic variations, including Average Nucleotide Identity (ANI), aligned portion, single nucleotide polymorphisms (SNPs), insertions and deletions (indels), and structural variants (SVs).

  • Phylogenetic Analysis
    Evolutionary relationship analysis based on conserved genes or whole-genome data. Outputs are provided in Newick (.nwk) format and as publication-ready images (.png).

Add-ons

  • Basecalling

    Conversion of raw sequencing signal data into nucleotide sequences using advanced basecalling algorithms. Includes quality optimisation for improved read accuracy and downstream genome assembly performance.

  • Repeat Annotation

    Identification and classification of repetitive genomic elements, including transposable elements, tandem repeats, and low-complexity regions, providing deeper insight into genome architecture and evolution.

  • Epigenomic Analysis

    Detection and analysis of epigenetic modifications, such as DNA methylation, directly from long-read sequencing data to reveal regulatory and functional genomic patterns.

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