De novo sequencing

This method is useful to build novel reference genomes, which could serve as a foundation for future research. Long-read technologies such as PacBio and ONT can decipher much of the structural properties of a genome. While PacBio HiFi assemblies do not need to be polished with short reads, Nanopore data requires an extra polishing step using Illumina data, e.g. paired-end libraries or HiC. HiC adds an additional layer of information to long-read data, arranges scaffolds in chromosomes and proofreads assembly quality.



NGI now offers de novo projects as one single package. Users can send in their sample(s) and NGI will take care of the separate library preparation setups suited for your particular project. A typical setup involves an initial draft genome assembled from long sequence reads, followed by scaffolding to get longer contigs and error-correction. This is followed by annotation of the new reference genome, eg. of genes and other functional elements. We also offer DNA extraction as a service for de-novo projects if required. For more info, please refer to our recent online webinar.

Project setup
In order to know how contiguous your assembly should be, please have a look at the flowchart.

Each study setup is described in more detail below. Once you have chosen the setup suitable for your de-novo project, the arrows direct you to the type of data you need. You can read more about the different technologies NGI offers to generate the data in the technology section below.

More info about what applications, methods and bioinformatics options NGI provides can be found further down.

All new projects should first be discussed with us prior to applications. Please contact us here.


Assembly
Methods for the initial sequencing of genomic DNA in order to build a draft genome reference.
Scaffolding
Methods to scaffold contigs together and correct genome assembly errors.
Annotation
RNA sequencing methods that can be used to annotate de-novo genomes with transcript locations.
Illumina TruSeq Stranded mRNA

RNA sequencing of mRNAs selected through poly-A enrichment.

Arima HiC

Production of high-quality proximity ligation libraries, using two restriction enzymes.

Dovetail Omni-C

A proximity-ligation protocol using a sequence-independent endonuclease, generating data for TAD identification and scaffolding.

Illumina Nextera DNA Flex

Low cost library preparation option for gDNA based on bead-linked transposase. Only for full plates of samples.

Illumina DNA PCR-Free

Method for shotgun DNA libraries used for whole genome sequencing and metagenomics.

Illumina TruSeq DNA PCR-free

Gold standard method for shotgun DNA libraries used for whole genome sequencing and metagenomics.

Illumina TruSeq DNA Nano

Library preparation from limited input DNA, used in whole genome sequencing and metagenomics etc.

SMARTer ThruPLEX DNA-seq

Library preparation for DNA, ideal for preparing libraries from small amounts of input material. Works well for shotgun libraries, ChIP DNA and FFPE samples, amongst others.

Loop Genomics sequencing

Loop genomics can provide both transcript counting and phasing for full length mRNA using short-reads on Illumina sequencers

Nanopore cDNA sequencing

Nanopore cDNA sequencing is able to sequence entire transcripts in one go, ideal for detecting isoforms and fusions events.

Nanopore DNA sequencing

Nanopore instruments can sequence very long continuous fragments of DNA. Sequencing native DNA allows detection of base modifications.

Nanopore Direct RNA sequencing

Nanopore direct RNA sequencing is able to sequence entire transcripts from native RNA, opening up opportunities to detect RNA modifications.

PacBio SMRT sequencing

PacBio SMRT sequencing generates reads tens of kilobases in length enabling high quality genome assembly, structural variant analysis, amplicon resequencing, full-length transcript isoform sequencing, full-length 16S rRNA sequencing and amplification free epigenetic characterization.

Falcon assemblies with CLR or HiFi data

NGI can generate high quality assemblies using PacBio CLR or HiFi data together with FALCON and FALCON-Unzip assemblers.

Nanopore analysis

Quality control, Basecalling and multiplexing of sequencing reads generated by Oxford Nanopore sequencers.

PacBio secondary analysis

Analysis applications provided by NGI using PacBio’s open-source SMRT Analysis software suite.

PromethION secondary analysis

Additional compute intensive nanopore raw data processing services provided by NGI

Illumina QC analysis

Basic quality-control monitoring of Illumina FastQ sequence data.