Covid-19 information

Please download our current information below:

MicrobesNG COVID-19 FAQs V4


If you would like to place an order, please request a quote online. If you are sequencing strains, we will send you a barcoded bead tube for each strain. Alternatively, you can send us extracted DNA (in which case we will only allocate barcode numbers for you to use). It is your responsibility to put the correct strain in each tube and return them to us. The tubes will be loaded onto our robot to perform DNA extraction and Illumina library preparation, and they will then be sequenced on an Illumina sequencer. The raw sequence data will be processed using our automated analysis pipeline, and returned to you via a website.

We want to provide affordable sequencing for all projects, no matter the size! We recognise that most sequencing providers want a long dialogue before you can actually get a quote. We are trying to simplify things by having a set competitive price.

Additionally, our costs are minimised due to extensive automation and economies of scale.

Currently, we charge £50 for BBSRC-funded projects, £70 for other non-commercial projects, and £100 for industrial projects. These prices are excluding VAT.

We aim to make the analysed sequence data available to you within eight to ten weeks of receiving the sample. You can see our live median wait time on the home page.

Yes, after an extremely successful five years of working within the University of Birmingham our BBSRC grant has come to an end and we are moving to bigger and better things.

We continue to work in close partnership with the University of Birmingham and are still based on the campus in the UoB research park.

The methods document below, covers all services:

MicrobesNG Genome Sequencing Service Methods

NOTE: Please do not send us any samples before you have received your barcodes/bead tubes. 

  • Here is our protocol for DNA submission:

MicrobesNG DNA preparation guide

  • Here is our protocol for Standard service strain submission (bead tube cryovials):

MicrobesNG preparing your bead tubes (Strains for Standard Service)

  • For our Enhanced service (EGS), please note that there are two sample preparation protocols available, depending on when your project was set up:

1. Preparing your samples in bead tube cryovials (for Enhanced projects set up before January 2021):

MicrobesNG Preparing your samples (Enhanced Genome Service)

2. Current protocol: preparing your samples in DNA/RNA shield inactivation buffer (for Enhanced projects from January 2021 onwards):

MicrobesNG Preparing your strains for EGS in DNA/RNA Shield

If we receive ambiguous samples that are not barcoded we cannot process these and we will have to destroy them.

Yes! If you have sequenced with us and acknowledge MicrobesNG in your publication we will give you a one free sample when you pay for 9 or more samples* (see below to find out how to acknowledge us)

Just email us with the DOI and project number, and we will do the rest:

*please note that only one voucher can be used per transaction and the voucher can only be applied to new orders.

We do not require co-authorship for our standard pipeline analysis. However, please make sure to acknowledge our service by including one of the following in the acknowledgements (depending on when you sequenced with us.

Pre September 2019:

Genome sequencing was provided by MicrobesNG ( which is supported by the BBSRC (grant number BB/L024209/1).

September 2019 onwards:

Genome sequencing was provided by MicrobesNG (

Such acknowledgements are critical to the long-term maintenance of the service.

If your project involves additional sequencing or bioinformatics not covered by our standard pipeline, then we may be able to help on a collaborative basis. In those circumstances, co-authorship would be expected.

If you acknowledge us we will give you a discount voucher (see the question above for details).


No, we are not currently licensed to handle any organisms not on our exclusion criteria. We can still provide you with a sequencing and analysis service, but you will have to perform the extractions yourself and send us DNA rather than the organism.

We strive to create an open, accessible community resource for researchers in the UK. As such it is important to us to make the sequence data publicly available. An embargo period can be put in place allowing you time to publish before the information becomes public.

Our embargo period is 12 months from when we send you your data. We are not in the position to negotiate with each individual group about the embargo. 

If you have data which you do not want to be made publicly available at all, you have that option to use our industrial rates of £100+VAT per sample.

Yes! We are now able to accept strains from outside the UK, providing that they comply with our submission criteria and are sent according to the appropriate postal regulations.

When preparing DNA extractions for sequencing with us, make sure they are eluted in EB buffer (i.e. 10 mM Tris-HCl pH 8.5) with no EDTA. Do not use TE for eluting the DNA as it contains EDTA, which inhibits our NGS library preparation. In the absence of a buffering agent, store samples at -25°C to -15°C to prevent degradation.


Currently, all sequencing for the Standard Sequencing Service is performed on the Illumina sequencing platform and for the Enhanced Genome Service we use Illumina and Oxford Nanopore sequencing platforms.

All projects will be sequenced using 2x250bp paired-end reads, regardless of what Illumina instrument is used.

Yes, with our Enhanced Genome Service (EGS). The EGS combines both Illumina short and Oxford Nanopore long read sequencing data to produce improved, and often fully complete and circularised, genome assemblies for bacterial strains.

No, currently MicrobesNG is focused on providing draft sequencing of microbial genomes as a sole application. However, our partner the University of Birmingham has performed the sequencing for projects using all of those methods, and may be interested in working on such projects on a collaborative basis outside of MicrobesNG. It should be noted that all of these methods typically require considerably greater sequencing depth than genome sequencing, so would be proportionally more expensive.

No, microbial genomes are much more interesting.


All projects are put through a standard analysis pipeline. We identify the closest available reference genome using Kraken, and map the reads to this using BWA mem to assess the quality of the data. We also perform a de novo assembly of the reads using SPAdes, and map the reads back to the resultant contigs, again using BWA mem to get more quality metrics.  

Upon receipt of a suitable reference (supplied by the user) we can predict variants relative to the reference. Variant calling is performed using VarScan. An automated annotation will be performed using Prokka. All data will be provided to you via a user-friendly web interface.

The MicrobesNG pipeline produces draft genome sequences, so you will not get back a closed genome. Repeat sequences larger than ~1000bp (e.g. IS elements and rRNA operons) cannot be resolved using our sequencing methods, and will cause a break in the assembly.

The number of contigs you will receive depends on the repeat structure of the genome. For an E. coli strain we would typically expect to obtain fewer than 200 contigs, with an n50 of >100kb (the n50 value means that at least half the genome is assembled into contigs of that size or greater).

The outputs from the analysis pipeline are provided using standard bioinformatics file formats including fasta, gbk, gff, fastq and finally, upon receipt of a reference genome from the customer, vcf and bam.

No, all samples are put through the same bioinformatics pipeline, which forms part of our QC procedure, and is provided at no additional cost. However, you will be able to download the raw sequence data in Fastq format, suitable for use with most downstream analysis tools (including BWA, Bowtie2, SPAdes and CLCBio).

MicrobesNG does not provide a bespoke analysis service, just the automated pipeline. However, we may be interested in helping on a collaborative basis.

Enhanced Genome Service (EGS)

For many organisms the answer is Yes, but it depends on the complexity and length of repeat regions in the genomes (and to a certain extent on the GC content of the organism). Simpler and shorter genomes are more likely to get complete assemblies. For more complex, longer and/or GC-skewed genomes circularization may not be possible but the assemblies will only have a few contigs (typically fewer than 10), compared to the tens or hundreds of contigs obtained with only Illumina short reads.

Indeed, this is one of the main applications of the EGS. By comparing complete (or nearly complete) EGS assemblies it is very easy to identify most, if not all, recombination regions, large inversions and insertions/deletions of variable size. These genomic features are very difficult or impossible to detect with short read Illumina assembles.

Most likely YES. However, for plasmids that have very similar genomes it is sometimes impossible to separate them even with a combination of long and short reads, and the assemblers may collapse them into one single plasmid.

Currently we only offer the EGS for bacterial strains (BSL1 or BSL2). We can only accept strains because we need do the DNA extractions in house to ensure the high purity and integrity required for the Oxford Nanopore long read sequencing. However we are working on ways to offer our EGS for DNA samples in the future.

Yes! We can now accept your strains from overseas, providing that they are complaint with the strain submission requirements on our website. You can see these when you request a quote.

You can expect the same Bioinformatics. For EGS projects you will receive annotation and assembly. We will also be able to perform variant calling if you provide us with a reference genome. 

No. We provide you with the Illumina and nanopore FastQ files but not the Fast5 data.

EGS is a hybrid assembly combining both Illumina and Nanopore reads. For this service we need to do a High Molecular Weight DNA extraction that requires a larger number of input cells. Due to this requirement our strain preparation protocol for the Enhanced Genome Service is different than for our Standard Genome Service.

In addition, to make sure that the data comes from exactly the same sample, we need to generate both Illumina and Nanopore sequencing from the same DNA. So, to generate the hybrid assembly for our Enhanced Genome Service we will need to perform the Illumina sequencing again and, unfortunately, we will not be able to use the previous Illumina data. 

Therefore we cannot offer a reduced price for the EGS even if you already have Illumina data for your sample from our Standard Genome Service.

Privacy Policy

The personal data we process is that which you provide to us. This is generally gathered from the completion of the online Quote Request Form, but may also be taken from other communications such as email, telephone and conferences.

The communications we send you will be tailored to any preferences you have expressed or derived from your use of our services to date.

MicrobesNG will keep your data indefinitely unless the customer specifically requests its permanent deletion.

MicrobesNG will process your personal data for the following purposes:

  • To prepare formal quotes, progress orders and manage financial transactions
  • To communicate in relation to all samples and sample progress
  • To ensure ongoing communications regarding existing projects and enquiries
  • With your consent to provide you with communications on our services, events and promotions
Information on how to exercise your right can be found through accessing our privacy information by following this link:

Privacy Policy