Genomics
Whole-genome sequencing, de novo assembly, and bioinformatic analysis of pure culture microbial genomes not only provide a detailed blueprint of the metabolic potential (genes and metabolic pathways) but is also often a prerequisite for studying gene expression patterns (transcriptomics or proteomics) and essential for high-resolution strain typing and comparative genomics.
We offer access to both short-read Illumina (MiSeq, HiSeq, and NovaSeq) and long-read (Oxford Nanopore) DNA sequencing platforms, allowing us to tailor sequencing and bioinformatic workflows according to your specific requirements. For reference-grade prokaryotic assemblies, we currently recommend using the current Oxford Nanopore long-read chemistry (R10.4.1, Kit V14). We do not recommend using a short read-only approach (e.g., Illumina). However, for the sequencing of eukaryotes, we recommend including short-read data (50x) for the final polishing of the assembled genome(s) (hybrid sequencing).
The team behind DNASense has extensive experience within the field of genomics, and our active involvement in state-of-the-art methods and sequencing platforms (read about it in Nature Methods) ensures that customers obtain valuable insight from our tailored bioinformatic analyses.
We have extracted DNA from all types of low- and high-biomass sample matrices. Our DNA extraction workflows can be customized (using both manual and automatic methods) to accommodate most sample types while minimizing DNA extraction biases in complex communities (see Albertsen et al.) and preserving yield and quality (purity and HMW DNA) to the widest possible extent. Our DNA extraction expertise guarantees the most optimal project outcome and is compatible with both short-read (Illumina) and long-read sequencing platforms (e.g., Oxford Nanopore sequencing).
Sample matrices (non-exhaustive list): Prokaryotes, invertebrates, fungi, salmon, wastewater, aquacultures, soil, oil spills, marine/freshwater samples, eDNA (environmental DNA), bioreactors, tree bark, mangrove and marine sediments, pig/chicken/rat/fish entrails/feces, mining/drill sites, cow rumen, seaweed, oysters, mouthwash, tooth swaps, skin swaps, microbial induced corrosion samples, lung tissue, colon cancer biopsies and liver biopsies.
Our standard package includes: Optional pre- and post-project meeting with a DNASense specialist, DNA extraction, library preparation, sequencing, pre- and post-sequencing quality control, de novo assembly, taxonomic profiling, gene annotation, rDNA extraction, access to raw data, result files and a detailed project report.
Add-on services (non-exhaustive list): Customized DNA extraction and purification, SNV/SV analysis, core genome SNP analysis, core genome MLST analysis, Functional annotation (KO, GO and KEGG), functional enrichment analysis, manual curation of metabolic pathways, gene mining, custom annotation and data submission.
FAQ
Which fast-track options do you offer?
Besides our standard TAT (3 weeks), we offer a fast-track option (5 work days) and an ultrafast-track option (24 hours). Both options are add-ons and special terms apply.
Should I send biomass or DNA?
We prefer biomass. Extracting high-quality DNA can be challenging and requires that you can evaluate the yield (Qubit dsDNA), purity (A260/A280 and A260/A230), and DNA size fragment distribution (e.g. on the Agilent Tapestation using Genomic ScreenTapes)
What level of taxonomic resolution can I expect from the classification?
For relatively complete prokaryotic genomes with little or no contamination, we use the Genome Taxonomy Database (GTDB), which potentially provides species-level resolution. Our standard service also includes rDNA extraction and classification against the Silva SSU database (genus level for both prokaryotes and eukaryotes). Custom databases can be included (add-on service).
Do you offer any guarantee with respect to Nanopore data yield?
Nanopore sequencing yield depends on many factors pertaining to the nature of the (native) DNA being sequenced. Therefore, we cannot offer any guarantee, but we regularly generate 20-30 Gbp on a single MinION run and 100+ Gbp on PromethION flow cells.
How long DNA fragments do I need for long-read sequencing?
It depends on the aim of your analysis. If you wish to produce closed genomes, your DNA read length distribution should be compatible with spanning the longest repeat element in your target genome. For bacteria, this is often the rRNA operon, i.e., reads should be able to span a length of 5000-7000 bp.
I have heard that Nanopore sequencing is error-prone?
The raw read accuracy of Nanopore sequencing is slightly lower than Illumina but we use state-of-the-art Q20+ chemistry which achieves comparable consensus accuracies and handles homopolymers found in prokaryotes (see Nature Methods).
Do you have an example report?
Yes. You can request an example report if you wish to see a typical project outcome
I want to retrieve a genome but my sample is non-axenic. How does this affect things?
If one or more contaminants are present in your sample, we would need to adjust the sequencing capacity to match the required depth of the targeted genome. If multiple genomes are present, consider our using our metagenomics service.
Case 1: We have extracted DNA from a pure culture bacteria and want to retrieve its 5 Mbp genome at 100x coverage. Therefore, we would need 5 Mbp x 100 x (100/10) = 5000 Mbp.
Case 2: We have extracted DNA from a non-axenic sample and want to retrieve a 5 Mbp genome at 100x coverage. The targeted genome (associated with our organism) is present at 10 % abundance. Therefore, we would need 5 Mbp x 100 x (100/10) = 5000 Mbp.
1000 Euro +
250 €/sample*
3 weeks standard turnaround time
7 days fast-track fee
1200 €
3 days fast-track fee
2000 €
Contact us about our Genomics service
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