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 assembly of more than 100 species’ genomes. Currently, over 70% of higher plant and animal genomes have been sequenced by BGI and its partners (including unpublished species).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 with polymerase length longer than 10kb
    • Guaranteed ≥20Gb/Cell PacBio Sequel II CCS(hifi library) data with accuracy greater than 99%
    • Guaranteed ≥14Gb/Cell PacBio Sequel data with polymerase length longer than 10kb
  • Turn Around Time

    Turn Around Time

    • For species with genome size ≤ 5Gb:

      -40 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
    • For species with genome size > 5Gb please contact us for accurate timelines.

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.

Sample type

Mass

Concentration

DNBSEQ 350bp library

≥1μg

20 ng/ul

DNBSEQ stLFR library

≥500 ng

1 ng/ul

Nanopore PromethION 20Kb library

≥10μg

100 ng/ul

PacBio Sequel II 20Kb CLR library

≥7μg

60 ng/ul

PacBio Sequel II 15Kb HIFI library

≥15μg

60 ng/ul

PacBio Sequel 20Kb de novo library

≥10μg

60 ng/ul

Concentration and Purity

Sample type

OD

Integrity (AGE)

DNBSEQ 350bp library

-

The band shown on gel electrophoresis has little degradation, or of fragment size greater than 20kb.

DNBSEQ stLFR library

OD260/280: 1.6-2.2 OD260/230: 1.6-2.2

The band shown on gel electrophoresis has little degradation, or of fragment size greater than 40kb.

Nanopore PromethION 20Kb library

OD260/280: 1.8-2.2 OD260/230: 1.8-2.2

The band shown on gel electrophoresis has little degradation, or of fragment size greater than 40kb.

PacBio Sequel II 20Kb CLR library

OD260/280: 1.6-2.2 OD260/230: 1.6-2.2

The band shown on gel electrophoresis has little degradation, or of fragment size greater than 40kb.

PacBio Sequel II 15Kb HIFI library

OD260/280: 1.6-2.2 OD260/230: 1.6-2.2

The band shown on gel electrophoresis has little degradation, or of fragment size greater than 40kb.

PacBio Sequel 20Kb de novo library

OD260/280: 1.6-2.2 OD260/230: 1.6-2.2

The band shown on gel electrophoresis has little degradation, or of fragment size greater than 40kb.

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 (Jellyfish + GenomeScope)

  • External pollution Analysis (BWA)

Genome Assembly

  • Reads correction

  • Assembly

  • Assembly result correction using long reads

  • Assembly result correction using short reads

  • BUSCO assessment

Gene Annotation

  • Repeat annotation

  • Gene prediction

  • Gene function Annotation

Evolution

  • Gene family identification (Animal TreeFam; Plant OrthoMCL; ≤10 species);

  • Phylogenetic tree construction

  • Estimation of divergence time

  • Genome synteny analysis

  • Whole genome duplication analysis

  • Gene family expansion and contraction analysis

  • Positive selection analysis

Auxiliary Assembly

Hi-C data auxiliary assembly

stLFR Assembly

  • Assembly using stLFR data

  • Gap filling

  • Super-Scaffold construction

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