De Novo Sequencing
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.
Aruna Science 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 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 Aruna Genomics specialist for details
Sample Requirements
Sample Purity: No contamination with RNA, protein or salt ions; colorless and transparent; non-sticky.
| Platform | Library Type | Mass | Concentration | OD | Integrity (AGE) |
|---|---|---|---|---|---|
| DNBSEQ | 350 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. |
| Nanopore | 20-50 Kb Normal long library | ≥2 μg | 50 ng/μL | OD260/280: 1.8-2.0 OD260/230：≥1.5 | The band shown on gel electrophoresis has no or little degradation. |
| Nanopore | Ultra long library | ≥10 μg | 50 ng/μL | OD260/280: 1.8-2.0 OD260/230：≥1.5 | The band shown on gel electrophoresis has no or little degradation. |
| PacBio Revio | 15-20 Kb HIFI library | ≥14 μg | 80 ng/μL | OD260/280: 1.6-2.2 OD260/230: 1.6-2.5 | The 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 Survey | 1.Kmer estimation (Jellyfish + GenomeScope); |
| Genome Assembly (Pacbio HiFi data) | 1. Assembly; 2. Assessment by short reads alignment; 3. BUSCO assessment ; |
| Gene Annotation | 1.Repeat annotation; 2.Gene structure annotation; 3.Gene function Annotation; |
| Evolution | Deliver 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 Assembly | Hi-C data auxiliary assembly |