Shotgun Metagenomics

Shotgun metagenomics analyses all genetic material within a sample, enabling comprehensive characterisation of entire microbial communities without the need for culturing. This approach reveals the taxonomic diversity, functional potential, and metabolic capabilities of microorganisms across complex environments. It is particularly powerful for microbiome research, environmental monitoring, pathogen discovery, and biotech innovation by providing deep insights into how microbial ecosystems function and interact.

Default Deliverables

  • Assembly & Gene Prediction Files

    FASTA format containing assembled metagenomic contigs or scaffolds reconstructed from shotgun sequencing reads.

  • Metagenome-Assembled Genomes (MAGs)

    Recovery and binning of draft microbial genomes from metagenomic assemblies, including genome completeness, contamination estimates, taxonomic classification, and quality assessment reports.

  • Taxonomic & Community Analysis

    Comprehensive microbial community profiling from shotgun metagenomic sequencing data, including taxonomic identification, relative abundance estimation, microbial diversity assessment, and comparative community analysis.

  • Predicted Gene Files

    • GFF3/GTF: gene coordinates and structural features

    • CDS sequences (FNA): nucleotide coding regions

    • Protein sequences (FAA): translated gene products

  • Functional Profiling

    Functional characterisation of metagenomic datasets, including Gene Ontology (GO), KEGG pathways, and EggNOG functional categories.

Base Pricing & Turnaround Time

Shotgun Metagenomics Analysis

Rp. 1.500.000 ($ 90) per sample

7 days

Additional charges may apply if the FASTQ file size is unusually large

Add-ons

  • Quality Control & Preprocessing

    • Basecalling

    • Host DNA Removal

  • Advanced Functional Analysis

    • Antimicrobial Resistance (AMR) Analysis

    • Virulence Factor Annotation

    • Plant Growth-Promoting Bacteria (PGPB) Analysis

    • Mobile Genetic Element (MGE) Analysis

    • Viral Metagenomics Analysis

    • CAZyme Annotation

    • MetaCyc Pathway Analysis

  • Comparative & Ecological Analysis

    • Biomarker Discovery

    • Time-series Community Analysis

    • Network & Co-occurrence Analysis

    • Differential Functional Enrichment Analysis

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