De Novo Sequencing

Description
Specification
Resources

Plant and Animal De Novo Genome Sequencing

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 small/large DNA fragments, assembling the reads into longer sequences (contigs) and finally ordering the contigs to obtain the entire genome sequence.

BGI Genomics is a recognized leader in De Novo Genome Sequencing and has extensive experience from the de novo sequencing and assembly of more than 400 species’ genomes. We offer a complete suite of technologies to support your de novo sequencing projects, along with expert assistance in the planning of optimal sequencing and bioinformatics options, to ensure your project is a success.

Project Workflow

We care for your samples from the start through to the result reporting. Highly experienced laboratory professionals follow strict quality procedures to ensure the integrity of your results.
  • SAMPLE PREPARATION
    Sample QC
  • LIBRARY CONSTRUCTION
    Library QC
  • SEQUENCING
    Sequencing QC
  • RAW DATA OUTPUT
    Data QC
  • BIOINFORMATICS ANALYSIS
    Delivery QC

Sequencing Strategy

De novo sequencing usually requires a customized approach based on your subject species’ genome size and complexity as well as the overall scientific objectives of the project.

Our plant and animal de novo sequencing services are usually performed using a combination of available platforms, including proprietary DNBSEQ™ platforms augmented with Nanopore, PacBio Revio for sequencing, library preparation and mapping. In addition, we offer extensive bioinformatics data analysis options for genome assembly, annotation and evolution studies.


Platform ToolsLibrary typeSequencingRecommend sequencing depth
DNBSEQ350bp LibraryPE150≥100X
Hi-C LibraryPE150≥100X
Nanopore PromethION20-40Kb LibraryRead length ≥10Kb30-100X
Ultra long library(>50K)Read length ≥20Kb30-100X
PacBio Revio15Kb CCS（HIFI） LibraryRead length ≥10Kb30-60X


Our Sequencing specialists will work with you to design the optimal strategies for your project, using platform combinations as appropriate for your project.


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Sequencing Service Specification

Our plant and animal de novo services are executed with multiple sequencing systems.

  • Sample preparation and services

    • Library preparations (DNBSEQ™, Nanopore, PacBio Revio etc)
    • Various sequencing platforms
    • Raw data, standard and customized data analysis
    • Available data storage and bioinformatics applications

  • Turn Around Time

    • Nanopore (normal library): Typical 30 working days from Sample QC acceptance to data analysis report availability
    • PacBio: Typical 30 working days from Sample QC acceptance to data analysis report availability
    • Case by case for the genome analysis
    • Expedited services are available; contact your local BGI Genomics specialist for details

  • Sequencing quality standard

    • Guaranteed ≥85% of DNBSEQ™ clean bases with quality score of Q30
    • Guaranteed ≥80 Gb PacBio Revio HiFi data except for some complex species

Sample Requirements

Sample Purity: No contamination with RNA, protein or salt ions; colorless and transparent; non-sticky.
PlatformLibrary TypeMassConcentrationODIntegrity (AGE)
DNBSEQ350 bp library≥0.2 μg (recommend≥0.4 μg)8 ng/μL-The band shown on gel electrophoresis has little degradation, or of fragment size greater than 20 kb.
Nanopore20-50 Kb Normal long library≥2 μg50 ng/μLOD260/280: 1.8-2.0 OD260/230：≥1.5The band shown on gel electrophoresis has no or little degradation.
NanoporeUltra long library≥10 μg50 ng/μLOD260/280: 1.8-2.0 OD260/230：≥1.5The band shown on gel electrophoresis has no or little degradation.
PacBio Revio15-20 Kb HIFI library ≥14 μg 80 ng/μLOD260/280: 1.6-2.2 OD260/230: 1.6-2.5The band shown on gel electrophoresis has no or little degradation. (The main peak is around 40 Kb with smear no smaller than 20 Kb)

Data Analysis

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


Service Content
Genome Survey1.Kmer estimation (Jellyfish + GenomeScope);
Genome Assembly (Pacbio HiFi data)1. Assembly;
2. Assessment by short reads alignment;
3. BUSCO assessment ;
Gene Annotation1.Repeat annotation;
2.Gene structure annotation;
3.Gene function Annotation;
EvolutionDeliver published genome and allied species (less than 10 species)
1.Gene family identification (Animal TreeFam; Plant OrthoMCL;≤10 species);
2.Phylogenetic tree construction;
3.Estimation of divergence time;
4.Genome synteny analysis;
5.Whole genome duplication analysis;
6.Gene family expansion and contraction analysis;
Auxiliary AssemblyHi-C data auxiliary assembly


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