Human Whole Genome Sequencing
Service Specifications
| Platform | Library | Sequencing Depth |
|---|---|---|
|
Illumina NovaSeq MGI DNBSEQ-T7 |
PE150 | ≥30 X |
| Nanopore PromethION 48 | 8 kb | ≥30 X |
| PacBio Revio | 15 kb - Hifi | ≥10 X |
Sample Requirements
| Platform | Concentration (ng/μL) | Total amount (μg) | OD260/280 | OD260/230 |
|---|---|---|---|---|
| Illumina/MGI PCR-free | ≥1 | ≥0.03 | - | Limited degradation and protein or RNA contamination |
| ≥40 | ≥0.5 | - | ||
| Nanopore | ≥40 | ≥4 | 1.7-2.2 | |
| PacBio | ≥50 | ≥10 | 1.7-2.2 |
Human Whole Exome Sequencing
Service Specifications
| Exon Capture Strategy | Sequencing Strategy | Recommended Data Output |
|---|---|---|
|
Sure Select Human All Exon v6 (Agilent) or xGen Exome Hybridization Panel v2 (IDT) |
Illumina NovaSeq PE150 |
5 - 10 Gb For mendelian disorders/rare diseases: > 50x For tumor samples: ≥ 100x |
Sample Requirements
| Sample Type | Amount (Qubit®) | Concentration | Volume | Purity (NanoDrop™) |
|---|---|---|---|---|
| Genomic DNA | ≥ 50 ng | ≥ 6 ng/μL | ≥ 15 μL |
OD260/280 = 1.8–2.0 no degradation, no contamination |
Plant/Animal Whole Genome Sequencing
Service Specifications
| Variants to be identified | Sequencing strategy | Recommended depth |
|---|---|---|
| SNP and InDel | Illumina NovaSeq PE150 or MGI T7 |
10x |
| SV and CNV (less accurate) | 30x | |
| SV and CNV (more accurate) | Nanopore Prom P48 | 20x |
| SNPs, Indels, SV and CNV | PacBio Revio | 10x |
Sample Requirements
| Tissue or extracted nucleic acids | Illumina/MGI | Nanopore | PacBio | ||
|---|---|---|---|---|---|
| Animal Viscera | 0.5 - 1 g | ≥ 3.5 g | ≥ 3.5 g | ||
| Animal Muscle | ≥ 5 g | ≥ 5 g | |||
| Mammalian Blood | 1.5 mL | ≥ 0.5 mL | ≥ 5 mL | ||
| Poultry/Fish Blood | ≥ 0.1 mL | ≥ 0.5 mL | |||
| Plant- Fresh Leaf | 1 - 2 g | ≥ 2 g | ≥ 5 g | ||
| Cultured Cells | ≥ 1×107 | ≥ 1×108 | |||
| Insect soft tissue/Individual | 0.5 - 1 g | ≥ 1 g | ≥ 3 g | ||
| Extracted DNA |
Concentration: ≥ 1 ng/μL Amount: ≥ 30 ng Limited or no degradation or contamination |
Concentration / Amount OD260/280 OD260/230 Limited or no degradation or contamination |
≥ 40 ng/ µL 4 µg/flow cell/sample 1.7 - 2.2 ≥ 1.5 |
Concentration / Amount OD260/280 OD260/230 Limited or no degradation or contamination |
≥ 50 ng/μL 10 μg/flow cell/sample 1.7 - 2.2 1.8 - 2.5 |
|
PCR-free Library Preparation: Concentration ≥ 40 ng/μL Amount ≥ 500 ng |
|||||
Plant/Animal De Novo Sequencing
Service Specification
| Genome survey | Genome assembly | Chromosome-level | Genome Annotation |
|---|---|---|---|
| 50X Illumina NovaSeq PE150 |
30X PacBio CCS HiFi reads |
100X Hi-C |
RNA-seq Illumina PE150 10 Gb + (optional) Full length RNA-seq PacBio 40 Gb or Nanopore 12 Gb |
Sample Requirements
| Tissue or extracted nucleic acids | Genome Survey | Genome Assembly with PacBio | Hi-C Assembly |
|---|---|---|---|
| Animal Viscera | 0.5–1 g | ≥ 3.5 g | ≥ 2 g |
| Animal Muscle | ≥ 5 g | ||
| Mammalian Blood | 1.5 mL | ≥ 5 mL | ≥ 2 mL |
| Poultry/Fish Blood | ≥ 0.5 mL | ||
| Plant - Fresh Leaf | 1–2 g | ≥ 5 g | ≥ 4 g |
| Cultured Cells | ≥ 1×108 | ≥ 1×107 | |
| Insect | 0.5–1 g | ≥ 3 g | ≥ 2 g |
| Extracted DNA |
Concentration: ≥ 1 ng/μL Amount: ≥ 30 ng Limited or no degradation or contamination |
Concentration: ≥ 50 ng/μL Amount: 10 μg/flow cell/sample OD260/280 = 1.7–2.2 OD260/230 = 1.8–2.5 Limited or no degradation or contamination |
– |
Bacterial and Fungal Whole Genome Re-Sequencing
Service Specifications
| Sequencing platform | Sequencing Strategy | Data recommended | Quality control |
|---|---|---|---|
| Illumina NovaSeq | PE150 | Depth of 100x | Q30 ≥ 85% |
Sample Requirement
| Concentration (ng/μL) | Total amount (ng) | Volume (μL) |
|---|---|---|
| ≥1 | ≥60 | ≥20 |
De Novo Bacterial Genome Assembly
Service Specifications
| Service | Sequencing Strategy |
|---|---|
| Draft Genome | Illumina PE150 100x |
| 0 Gap Genome | Nanopore 100x + Illumina PE150 100x or Pacbio HiFi 30x + Illumina PE150 100x (optional) |
Sample Requirements
| Concentration (ng/μL) | Total amount (μg) | Volume (μL) | OD260/280 | OD260/230 | |
|---|---|---|---|---|---|
| PacBio | ≥ 20 | ≥ 1.2 | ≥ 20 | 1.7-2.2 | ≥ 1.0 |
| Nanopore | ≥ 40 | ≥ 2 | ≥ 20 | 1.7-2.2 | 1.0-3.0 |
| Illumina | ≥ 1 | ≥ 0.06 | ≥ 20 | - | - |
De Novo Fungal Genome Assembly
Service Specifications
| Service | Sequencing Strategy | Quality Control |
|---|---|---|
| Draft Genome | Illumina PE150 | Q30 ≥ 85% |
| Fine Genome | Nanopore 50x + Illumina PE150 50x Assembly: PacBio HiFi 30x or Nanopore 100x + Illumina PE150 50x or Hi-C Assembly 100x | contig N50 ≥ 1 Mb; contig N50 ≥ 500kb (fungi) |
Sample Requirements
| Concentration (ng/μL) | Total amount (μg) | Volume (μL) | OD260/280 | OD260/230 | |
|---|---|---|---|---|---|
| PacBio | ≥ 20 | ≥ 1.2 | ≥ 20 | 1.7-2.2 | ≥ 1.0 |
| Nanopore | ≥ 40 | ≥ 2 | ≥ 20 | 1.7-2.2 | 1.0-3.0 |
| Illumina | ≥ 1 | ≥ 0.06 | ≥ 20 | - | - |
16S/18S/ITS Amplicon Sequencing - PacBio
Service Specifications
| Library | Sequencing Strategy | Data Recommended |
|---|---|---|
| Amplicon | PacBio Revio | 10/30/50 K tags (CCS) |
Sample Requirements
| Concentration (ng/μL) | Total amount (μg) | Volume (μL) |
|---|---|---|
| ≥ 5 | ≥ 0.3 | ≥ 20 |
16S/18S/ITS Amplicon Sequencing – Illumina NovaSeq
Service Specifications
| Library | Sequencing Strategy | Data recommended |
|---|---|---|
| Amplicon | Illumina PE250 | 50/100/300K tags (Read Pairs) |
Sample Requirements
| Concentration (ng/μL) | Total amount (ng) | Volume (μL) |
|---|---|---|
| ≥ 1 | ≥ 200 | ≥ 20 |
Metagenomic Sequencing
Service Specifications
| Sequencing platform | Sequencing Strategy | Data recommended |
|---|---|---|
| Illumina NovaSeq | PE150 | 6 Gb |
| Nanopore P48 | 10 kb | 6 / 10 Gb |
| PacBio Revio | 8 kb | 10 / 20 Gb |
Sample Requirements
| Library | Concentration (ng/μL) | Total amount (μg) | Volume (μL) |
|---|---|---|---|
| Illumina PE150 Library | ≥ 1 | ≥ 0.03 | ≥ 20 |
| Nanopore 10 kb Library | ≥ 40 | ≥ 2 | ≥ 20 |
| PacBio 8 kb Library | ≥ 50 | 10 μg/cell | ≥ 20 |
Specific-Locus Amplified Fragment Sequencing (SLAF-Seq)
Service Specifications
| Type of analysis | Recommended population scale | Sequencing strategy | Tag number |
|---|---|---|---|
| Genetic Maps | 2 parents and >150 offspring | Parents: 20x WGS Offspring: 10x |
Genome size: <400 Mb: WGS recommended <1 Gb: 100K tags 1-2 Gb: 200K tags >2 Gb: 300K tags Max 500K tags |
| Genome-Wide Association Studies (GWAS) | ≥ 200 samples | 10x | |
| Genetic Evolution | ≥ 30 samples, with ≥ 10 samples from each subgroup | 10x |
Service Requirements
- Concentration ≥ 5 ng/μL
- Total amount ≥ 80 ng
- Nanodrop OD260/280 = 1.6 – 2.5
- Agarose gel: No or limited degradation or contamination
Hi-C Based Genome Assembly
Service Specifications
| Library preparation | Sequencing strategy | Recommended data output | Quality control |
|---|---|---|---|
| Hi-C library | Illumina NovaSeq PE150 | 100x | Q30 ≥ 85% |
Sample Requirements
| Tissue | Required amount |
|---|---|
| Animal Viscera | ≥ 2 g |
| Animal Muscle | ≥ 2 g |
| Mammalian Blood | ≥ 2 mL |
| Poultry/Fish Blood | ≥ 2 mL |
| Plant - Fresh Leaf | ≥ 3 g |
| Cultured Cells | ≥ 1×107 |
| Insect | ≥ 2 g |
Genome-Wide Association Analysis (GWAS)
Service Specifications and Sample Requirements
| Type of sequencing | Recommended population scale | Sequencing strategy | Nucleotide requirements |
|---|---|---|---|
| Whole Genome Sequencing | 200 samples | 10x |
Concentration ≥ 1 ng/μL Total amount ≥ 30 ng Limited or no degradation or contamination |
| Specific-Locus Amplified Fragment (SLAF) |
Tag depth: 10x Number of tags: < 400 Mb: WGS recommended < 1 Gb: 100K tags 1-2 Gb: 200K tags > 2 Gb: 300K tags Max 500K tags |
Concentration ≥ 5 ng/μL Total amount ≥ 80 ng Nanodrop OD260/280 = 1.6–2.5 Agarose gel: no or limited degradation or contamination |
Evolutionary Genetics
Service Specifications and Sample Requirements
| Type of sequencing | Recommended population scale | Sequencing strategy | Nucleotide requirements |
|---|---|---|---|
| Whole Genome Sequencing | ≥ 30 individuals, with ≥ 10 individuals from each subgroup | 10x |
Concentration ≥ 1 ng/μL Total amount ≥ 30 ng Limited or no degradation or contamination |
| Specific-Locus Amplified Fragment (SLAF) |
Tag depth: 10x Number of tags: < 400 Mb: WGS recommended < 1 Gb: 100K tags 1-2 Gb: 200K tags > 2 Gb: 300K tags Max 500K tags |
Concentration ≥ 5 ng/μL Total amount ≥ 80 ng Nanodrop OD260/280 = 1.6–2.5 Agarose gel: no or limited degradation or contamination |
Comparative Genomics
Service Specifications
| Estimated turn-around time | Number of species | Analyses |
|---|---|---|
| 30 working days | 6 - 12 |
Gene family clustering Gene family expansion and contraction Phylogenetic tree construction Divergence time estimation (Fossil calibration required) LTR insertion time (For plants) Whole genome duplication (For plants) Selective pressure Synteny analysis |
Sample Requirements and Delivery
| Species | Tissue | Survey | PacBio CCS |
|---|---|---|---|
| Animal | Visceral tissue | 0.5 ~ 1 g | ≥ 3.5 g |
| Muscle tissue | ≥ 5.0 g | ||
| Mammalian blood | ≥ 5.0 mL | ||
| Poultry/Fish blood | - | ≥ 0.5 mL | |
| Plant | Fresh Leaf | 1 ~ 2 g | ≥ 5.0 g |
| Petal/Stem | 1 ~ 2 g | ≥ 10.0 g | |
| Root/Seed | 1 ~ 2 g | ≥ 20.0 g | |
| Cells | Cultured cell | - | ≥ 1 × 108 |