Genome Assembly (de novo)

De novo genome assembly reconstructs a complete genome directly from raw sequencing reads, without relying on any reference genome. This approach is essential for exploring previously uncharacterized organisms, uncovering novel genetic architectures, and capturing unique structural variations that reference-based methods may miss. It is particularly powerful for biodiversity studies, microbial discovery, and advancing biotech innovation through truly original genomic insights.

Base Pricing & Turnaround Time

Procaryote Genome

Rp. 1.000.000 ($ 60) per sample

7 days

Eucaryote Genome

Start from: Rp. 1.200.000 ($ 70) per sample

7 days

small-size genome (<150Mbp)

Eucaryote Genome

large-size genome (>150Mbp)

Start from: Rp. 2.000.000 ($ 120) per sample

7 days

Default Deliverables

  • Assembled Genome
    FASTA format containing high-quality contigs, scaffolds, or chromosome-level assemblies.

  • Assembly Metrics Report
    Comprehensive quality assessment including N50/L50, total genome size, GC content, and genome completeness (BUSCO).

  • 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.

  • Hybrid Assembly

    Integration of short-read and long-read sequencing data to generate highly accurate and contiguous genome assemblies with improved completeness and reduced error rates.

  • Chromosome-level Scaffolding

    Construction of chromosome-scale genome assemblies using long-range genomic information such as Hi-C or optical mapping data, enabling highly ordered and biologically meaningful genome structures.

  • 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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