De novo Genome assembly and Annotation Solution

Generate reference-quality genomes and annotations for your organisms of interest

Genome assembly, annotation and analysis

End-to-end solution

The ability to generate chromosome-level genomes or sequence-specific genomic regions of interest has tremendous implications for a variety of applications. MedGenome solutions are being used across development, disease, evolution, and crop breeding. We offer a complete end-to-end workflow that enables researchers to sequence, assemble and annotate reference-quality genomes at scale. Our comprehensive genome annotation pipeline, GenomeSlayer, combines several best-in-class annotation algorithms and visualization tools to generate publication-ready analysis outputs. Get access to our latest cutting-edge technologies such as long read sequencing (PacBio HiFi, Oxford Nanopore) and Arima Hi-C.

Advantages of the MedGenome approach

Entrust your genome project to our experienced team

Our comprehensive solution delivers fast turnaround times from sample preparation to publishable genome assembly and annotation.

  • Streamlined computational workflows for fast & scalable analysis.
  • Customized interactive reports.
  • Publication-ready figures.
  • Expert, hands-on data interpretation support.
Case study

The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins

See how MedGenome solutions enabled mapping the 'venome-ome' in Naja naja Indian cobras.
MedGenome Genome Assembly

Specifications and deliverables

Choose the genomic workflow that works for you

Delivery time

Contact us to find out more

Sample requirements

  • A tissue sample of sufficient quality.
  • Any species-specific information if known a priori (e.g. estimated genome size, ploidy, number of chromosomes).
  • Additional samples may be provided to generate Illumina RNA-seq and PacBio full-length transcriptome data.

Sequencing platforms

PacBio, Illumina®

Analysis platforms

HiFiasm, Juicer, 3D-DNA, Merqury, MAnGO and GenomeSlayer

Project Deliverables

All genome assembly and annotation deliverables include:

  • All short-read and long-read sequencing data generated (PacBio DNA and RNA-seq, Illumina RNA-seq and Hi-C).
  • BAM files(s) containing alignments of the Hi-C library read pairs mapped to the draft assembly.
  • QC report.
  • The primary haplotype assembly in FASTA format.
  • A report summarizing key assembly statistics, features of the Hi-C library, and a linkage density plot of the proximity ligation library data.
  • A table detailing the breaks made to the input scaffolds.
  • A table describing the position of the input assembly scaffolds within the final Hi-C scaffolds.
  • Chromosomal-level scaffolded genome assembly and assembly statistics.

TAD Analysis deliverables, if requested, include:

  • TAD calls at 10 kbp, 25 kbp, and 50 kbp.
  • CTCF binding sites.
  • A/B compartmental organization.
  • Isochore locations.
  • Output files for visualizing TADs using HiGlass.
  • Summary report.

Genome annotation deliverables include:

  • Genome annotation and quality assessment statistics.
  • Repetitive element annotation and statistics.
  • Genome annotation file in GFF3 format.
  • Repeat annotation file in GFF3 format.
  • Functional annotation file in tabular format.
  • Predicted gene CDS sequences in FASTA format.
  • Predicted gene peptide sequences in FAST format.
  • Alignment files from RNA-seq and Iso-Seq data in BAM format (if data is generated or provided).
  • Visualization of structures of manually curated genes.

Advanced annotation deliverables include:

  • Custom gene family annotation.
  • Custom analysis pipelines.
  • Differential gene expression analysis.
  • Whole genome comparative analysis.

Our publications

Go deeper

Suryamohan, K., et al. The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins. Nat Genet 52, 106–117, 2020.
Shukla, H., et al. Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex predation, GigaScience, Volume 12, 2023.
Bernard, K.B., et al. Genetic Variation in Reproductive Investment Across an Ephemerality Gradient in Daphnia pulex, Molecular Biology and Evolution, Volume39, Issue 6, June 2022.


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