Microbiome analysis
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PacBio and Oxford Nanopore sequencing
Long-read sequencing can determine the nucleotide sequence of long sequences of DNA, roughly between tens and hundreds of thousands of base pairs. This removes the need to cut and amplify DNA (which is a standard procedure for short-read sequencing by Illumina).
There are several long-read sequencing technologies commerically available and continuously being developed. Of these, we offer the following two:
| Technology | PacBio | Oxford Nanopore (ONT) |
| Applications | Genome assembly - Analysis of repeats, structural variations - Sequencing of longer amplicons eg 16S rRNA gene - Full-length transcripts, alternative splicing | Genome assembly - Sequencing of longer amplicons eg 16S rRNA gene |
| Project type | Can be combined with short reads by Illumina. Rather larger projects with a higher price. | We highly recommend to combine ONT with short-reads by Illumina. Rather small to medium projects with a lower total cost. |
| Available sequencing settings | Variable, see our pricelist or contact us | |
| Capacity | Sequel II: 300-350 Gb HiFi* | MinION: 1-10 Gb |
| Sequencing errors | Low error rate in HiFi mode (<1%), higher error rate in CLR mode. Random errors. |
Relatively high-error rate. Systematic errors. |
| Guarantee | The amount of data output is approximate. | |
| Library preparation | We do not allow preparation of libraries by our clients. | |
| Library type | No limits | |
| Outputs | Standard (commonly used data formats etc.) | |
* PacBio technology is capable of producing up to several hundred kilobases of sequence length, and sequencing accuracy can be as high as 99.5%. Unfortunately, the maximum length and quality cannot be achieved at the same time. If the user seeks high-quality data, approx. 15kb long reads can be obtained. On the other hand, achieving several tens to hundreds of kilobases long reads is possible, but with a reading accuracy of only approx. 90-95%.
Genome assemblyIn our lab these technologies are primarily requested by customers interested in assembling new genomes (but not necessarily). Genome assembly is the computational process of deciphering the sequence composition of DNA within the cell of an organism, using short or long (or both) sequencing reads. It can be described as solving a jigsaw puzzle. The DNA fragments (pieces) produced by long-read sequencing are easier to assemble into a complete DNA sequence simply because they are longer, same as jigsaw puzzle with less larger pieces. This makes the long-read sequencing the technology of choice for this task. However, due to lower data quality of long-read technologies overall it is beneficial to think of combining them with Illumina short reads. Read about genome assembly by using data from Oxford Nanopore and Illumina technologies! |
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Full-length 16S sequencingWhen identifying some bacterial species, eg in complex communities, Illumina amplicon sequencing is insufficient and the entire 16S rRNA gene needs to be sequenced. PacBio technology, for example, is particularly suitable for this approach. Technologically, it is similar to any amplicon sequencing. Special primers compatible with sequencing on a Sequel instrument are used and up to 190 samples can be multiplexed into one sequencing library. We will arrange the entire process for you on a turnkey basis, including long-range PCR on the gDNA supplied by you.
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For PacBio/ONT technologies, we do not allow preparation of libraries by our clients. You must supply DNA/RNA.
Once the sequencing run is finished, you will receive its standard outputs from us. Because each sequencing project has specific data analysis requirements, we offer turnkey data analysis for the needs of your project - Custom Data Analysis. Our bioinformaticians can help you with any data analysis goal. If you are interested in this service, individual consultation is required, we recommend you seek our help already at the project preparation stage.
Approx. 6 weeks (data analysis not included)
If you are new to NGS, we encourage you to attend our two-day NGS introductory course. We will be happy to welcome you on some of other courses and workshops too.
If you want to order these services, please contact us to get a price quotation.