Plant & Animal De Novo Whole Genome Sequencing

Plant & Animal De Novo Whole Genome Sequencing

Service Description

De novo sequencing refers to the sequencing of a novel genome without a reference sequence for alignment. The process of de novo genome sequencing involves the sequencing of DNA fragments, assembling the reads into longer sequences (contigs) and finally ordering the contigs to obtain the entire genome sequence.

BGI is a recognized leader in de novo Whole Genome Sequencing and has extensive experience from the de novo sequencing and published more than 400 species’ genomes. Currently, more than 1000 plant and animal genomes have been sequenced by BGI and its partners (including unpublished species)

We offer a complete suite of technologies to support your de novo sequencing projects, along with expert assistance with the planning of optimal sequencing and bioinformatics options, to assure your project is a success.

Project Workflow

We care for your samples from receipt through to result reporting. Highly experienced laboratory professionals follow strict quality procedures to ensure the integrity of your results.

  • Sample acceptance and QC
  • Library QC
  • Data QC
  • Project evaluation and planning
  • Construction of Libraries
  • Sequencing on multiple platforms
  • Genome Assembly
  • Genome Annotation and Evolution study

How to order

Request a Quote

Send us a no obligation request for quote and our dedicated sales team will reply to you within 24 hours.

Create an Online myBGI Account

Create a myBGI account to view all our sample and shipping documentation and to manage your project moving forwards. It's quick, free and easy!

Sequencing Service Specification

BGI provides various combinations of sequencing platforms, sequencing read-lengths and paired-end library options for De Novo sequencing applications for plant, animal and microorganisms.For microorganisms, BGI only provides library construction and sequencing for De Novo whole genome sequencing applications.

Services are performed on DNBSEQ™, Illumina, Nanopore PromethION, PacBio Sequel II or Sequel platforms.

  • Sample Preparation and Services

    Sample Preparation and Services

    • Library preparation (DNBSEQ™, Illumina, Nanopore PromethION, PacBio Sequel II)
    • Various sequencing mode
    • Raw data, standard and customized data analysis
    • Available data storage and bioinformatics application
  • Sequencing Quality Standard

    Sequencing Quality Standard

    • Guaranteed ≥90% of DNBSEQ™ clean bases with quality score of Q20
    • Guaranteed ≥50Gb/Cell Nanopore pass data with polymerase length longer than 10kb
    • Guaranteed ≥100Gb/Cell PacBio Sequel II CLR data
    • Guaranteed ≥20Gb/Cell PacBio Sequel II CCS(hifi library) data with accuracy greater than 99% except some complex species
  • Turn Around Time

    Turn Around Time

    • For the species with genome size ≤ 5Gb:

      -70 working days from sample QC acceptance to filtered data availability;

      -40/70 working days for the bioinformatics of common/complex genome assembly;

      -30 working days for the bioinformatics of genome annotation;

      -30 working days for the bioinformatics of genome annotation
    • Case by case for the species with genome size > 5Gb.

Note: The total quantity of sample required is also determined by the experimental strategy, as well as the type and number of libraries to be constructed.

PLATFORM SAMPLE TYPE MASS CONCENTRATION OD INTEGRITY (AGE)
DNBSEQ stLFR library ≥500 ng ≥1ng/μL OD260/280: 1.6-2.2 OD260/230: 1.6-2.2 No degradation or little degradation with main band≥40Kb
350bp library ≥1μg ≥12.5ng/μL No degradation or little degradation with main band≥20Kb
Nanopore PromethION 20-40Kb library ≥9μg ≥90ng/μL OD260/280: 1.6-2.2 OD260/230: 1.6-2.2 No degradation or little degradation with main band≥40Kb
Ultra-long library(>40K) ≥10μg ≥100ng/μL No degradation or little degradation with main band≥50Kb
PacBio Sequel II 15-20Kb HIFI library ≥15μg ≥80ng/μL OD260/280: 1.6-2.2 OD260/230: 1.6-2.5 No degradation or little degradation with main band≥30Kb
20-40Kb CLR library ≥7μg ≥80ng/μL No degradation or little degradation with main band≥40Kb
40-60Kb CLR library ≥9μg ≥80ng/μL No degradation or little degradation with main band≥50Kb

Data Analysis

Besides clean data output, BGI offers a range of standard and customized bioinformatics pipelines for your plant and animal de novo sequencing project.
Reports and output data flies are delivered in industry standard file formats: BAM, .xls, .png. Raw FASTQ and FASTA data is available.

Genome Survey

  • Kmer estimation;

  • External pollution Analysis;

Genome Assembly (PacBio HiFi reads)

  • Assembly;

  • Assessment by short reads alignment;

  • BUSCO assessment;

Genome Assembly (PacBio CLR/ Nanopore reads +NGS)

  • Reads correction;

  • Assembly;

  • Assembly result correction using long reads;

  • Assembly result correction using short reads;

  • BUSCO assessment;

Auxiliary Assembly

Hi-C data auxiliary assembly;

Gene Annotation

  • Repeat annotation;

  • Gene prediction;

  • Gene function Annotation;

Evolution

  • Gene family identification (≤10 species);

  • Phylogenetic tree construction;

  • Estimation of divergence time;

  • Genome synteny analysis;

  • Whole genome duplication analysis;

  • Gene family expansion and contraction analysis;

  • Transcription factor prediction;

  • Specific gene family analysis;

stLFR Assembly

Genome assembly using stLFR data

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