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

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• 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.

PacBio, Illumina®

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

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.