Whole Genome Sequencing

Plasmidsaurus Whole Genome Sequencing is performed using the newest long-read sequencing technology from Oxford Nanopore Technologies (ONT).

We use a transposome complex to construct an amplification-free long-read sequencing library, including minimal fragmentation of the input genomic DNA in a sequence-independent manner, and return you the annotated genome assembly. For more details on our workflows and bioinformatics pipelines, please see technical documentation for Whole Genome Sequencing. 

Our bacterial, yeast, and eukaryotic services offer similar library preparation and sequencing quality but specialized genome extraction services, sequencing depth, and bioinformatics pipelines optimized for bacteria, yeast, and eukaryotes (including filamentous fungi and multicellular animals). 

We recommend choosing the option that matches the organism you are sequencing. If you need more read depth for yeast sequencing, you can submit yeast samples to the Eukaryotic genome services that offer higher data targets. Deeper sequencing is also available for multicellular genomes via our Custom Service. 

The Hybrid ONT + Illumina option for Bacteria and Yeast Genome Sequencing polishes your long-read ONT assembly with Illumina short reads (paired-end 2x150bp) using the Polypolish v0.6 tool to improve the consensus quality at those tricky homopolymer runs and methylation motifs. 

This Hybrid service is ideal when:

• You anticipate an abundance of homopolymers and/or methylated motifs in the genome
• You are planning to use the genome assembly result as a reference for SNP variant calling

The Hybrid service is not generally necessary if your primary goal is to obtain a high quality, high coverage, highly contiguous genome assembly, as contiguity is entirely determined by the quality and quantity of the ONT long read data. Adding in short Illumina reads with the Hybrid service has no impact on the number, size, or topology of assembled chromosomes/elements, and instead only improves nucleotide-level basecalling accuracy in homopolymers and methylated motifs via polishing. For this reason, we do not repeat the genome assembly or contig identification workflows after Illumina polishing.
 
Please note: Hybrid ordering options are not currently available for the Eukaryotic Genome, but you can request to add Illumina data to your ONT eukaryotic data through the Custom Sequencing service.

The Eukaryotic Genome Sequencing service offers four different service levels,  which allow you to select the target amount of output per sample, measured in Gb of fastq data. We don't specify output in number of reads because that varies based on the specific read length distribution in question. 

The Service Level recommendations below are based on a target of approximately 30x genome coverage, which is typically sufficient to generate a high-quality de novo genome assembly with annotations. Depending on your application, you can submit your sample to a different service level than is recommended in order to obtain a different amount of coverage. For example:

• If you plan to use the raw reads to perform copy number variant analysis against a reference genome, you might need less genome coverage, e.g. 10-20x. Please note that while the assembly is more likely to fail at lower coverage levels, you will still be able to use the raw reads to perform your analysis
• If you plan to use the raw reads to generate a haplotype-phased de novo genome assembly, in some cases you might need more genome coverage, e.g. 60-100x

The typical turnaround time in business days is listed below for each service. This is the average time it takes to return data to customers who are submitting orders from US, UK and EU. Turnaround times for customers in APAC may be slightly longer due to the time required in transit to our lab in Singapore.

Low sample quality can also negatively impact turnaround time and the quality of your results. Please read sample prep instructions carefully to make sure your samples meet input requirements. Due to variability in shipping logistics and sample quality that is outside our control we cannot guarantee turnaround times or sample success rates.