Short Read Service

This service is open to all microbes via a DNA submission, and if you are working with bacteria you can choose to send us strains instead, and we’ll handle the DNA extraction at no extra cost!

We use 250 bp paired end sequencing to provide the absolute highest quality assemblies of your genomes, and we make things as simple as possible, offering a minimum of 30X coverage (i.e. on average, each position in the genome is sequenced 30 times) - if we don’t hit that, we’ll repeat the sequencing at no extra charge. See our resequencing guidelines for details.

Service Overview

We charge £65 Ex. VAT for genomes up to 10 Mb in length, and can sequence any organism up to 50 Mb in length; each additional 10 Mb is charged at £32.50 Ex. VAT.

Our standard guaranteed coverage is 30X, which is suitable for whole genome assembly and variant calling. For deep sequencing applications, you can increase the target coverage all the way up to 510X: each additional 30X coverage is also charged at £32.50 Ex. VAT.

We have excellent volume discounts available, meaning Short Read can be purchased for as little as £45.50 Ex VAT per sample.

Our target turnaround time is 4-7 weeks from sample receipt.

Send Us

We accept DNA from any microbial organism. Your DNA will need to meet some basic quality standards - you can see our submission protocol for DNA here:

• DNA Submission Protocol

If you work with bacteria, we can handle the DNA extraction for you at no extra cost. All you need to do is grow your strains, and place 10⁶ - 10⁹ cells into buffer tubes that we provide, you can see our submission protocol here:

• Strain Submission Protocol

Service Outputs

Your data will be delivered via a secure project portal, which can be shared with collaborators and key stakeholders. Your data will be stored for a minimum of 12 months.

The outputs will include:

• 2 x 250 bp Illumina reads in .fastq format
  • Allows you to perform your own analysis and upload to public repositories.
• A draft de novo assembly of your genome in .fasta format
  • Allows you to query your genome for key information, can be used in various downstream analyses.
• Annotations in genbank (.gbk) and .gff formats
  • Allows you to look at the CDS identified in your genome.
• Taxonomic classifications of your reads and assembly
  • Provides 16S and species identification to confirm your sample is pure.

Good applications

Short read is a great fit for the majority of sequencing projects; it’s the bread and butter service that lets you accomplish several analyses at a value driven price. It’s particularly good for short variant detection (e.g. SNP-based outbreak analyses), and for resequencing projects (e.g. experimental evolution) where you have a reference genome you can compare your data to.

Bad applications

Short reads produce fragmented genomic assemblies, with the chromosome split into several pieces (10’s to 100’s, depending on the organism). De novo assembly of mobile genetic elements like plasmids is also very challenging with short reads alone. If assembly contiguity and recovery of mobile genetic elements is important to your work, then you’d be better with our Long Read service.

If you are looking for a reference quality genome, then our Hybrid service is the best option; it combines our Short and Long read services to get the best of both worlds; high assembly completeness from the long reads, and high sequence accuracy from the short reads.

If you’re just trying to classify a ≤30 Kb plasmid from a cloning experiment, then Long Read and Hybrid will be overkill. Check out our PlasmidSeq service, which costs just £10 Ex. VAT!

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