Top 3 most commonly asked questions!

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

Here are our protocols organised by service:

Standard Service

  • DNA Samples
Preparing DNA samples

  • Strain Samples
Inactivation buffer (Projects created from 21st May 2021)

Bead tubes (Projects created prior to 21st May 2021)


Enhanced Service

Inactivation buffer (Projects created from January 2021)

Bead tubes (Projects created prior to January 2021)


The relevant protocol will have been provided to you in the email we sent you when your project was set up. If you have any doubt as to which protocol relates to your project, please email us on info@microbesng.com and state your project reference number.

We aim to make the analysed sequenced data available to you within 8-10 weeks of receiving the sample. You can see our live median wait time on our home page. If you have a specific requirement for project completion, let us know and we will see what we can do. Just email us on info@microbesng.com.

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.

Covid-19 information

Please download our current information below:

MicrobesNG COVID-19 FAQs V4

Quotes, Ordering and Payment

Please request a quote online. If you are happy with the quote then you can then proceed with payment as explained in the email you will receive along with your quote, to place an order.

Any details that you want us to be aware of, please put in the comments section of the quote request form.

There are two ways that you can place your order / make payment:

Online payment

You can pay online via credit card, using the link that was emailed to you along with your quote.

Invoice

  1. If you would like to receive an invoice in relation to your order please forward us a Purchase Order document (with full contact information of your Accounts Payable Department and VAT registration number) to our info@microbesng.com email address. 
  2. If you would like to receive an invoice, but your institution does not use a PO system we will need the following information to arrange for an invoice:

  • Full institution name, postal address and email for where you would like the invoice sent.
  • VAT registration number.
  • Any grant code/ reference number that you need to appear on the invoice.
* Please note that MicrobesNG is our Trading name and Microbial Genomics Ltd is our Registered name. Your purchasing system may have us set up under either of these names *

Only after you’ve arranged payment or provided the invoicing information as described above and we have sent you your barcodes, can you send us your samples.

See our Homepage for a full breakdown of prices and if you have any questions please email us at info@microbesng.com. If you would like a quote, please fill in a brief online quote request form.

Yes! We have a proven track record of delivering high volume orders on time, providing high quality data and an excellent customer experience.

If you have a project that you consider high volume, please contact us on info@microbesng.com and we can help find the solution that best suits your project needs.

You can register as a user by clicking at the top right tab on our website “Register”.

By doing this, you will be able to see in one page all of the different projects you might have with us and also add/ remove collaborators and grant them access to individual projects. Please make sure to use the exact same email address that you have used to communicate with us and to request quotes.

Samples

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

Here are our protocols organised by service:

Standard Service

  • DNA Samples
Preparing DNA samples

  • Strain Samples
Inactivation buffer (Projects created from 21st May 2021)

Bead tubes (Projects created prior to 21st May 2021)


Enhanced Service

Inactivation buffer (Projects created from January 2021)

Bead tubes (Projects created prior to January 2021)


The relevant protocol will have been provided to you in the email we sent you when your project was set up. If you have any doubt as to which protocol relates to your project, please email us on info@microbesng.com and state your project reference number.

We are now able to accept GMM strains from anywhere in the world, thanks to our newly launched strain submission protocol!

Our full strain submission criteria can be found in our quote request form.

No, we are not currently licensed to handle any organisms 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 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.

Our Sending Your Samples Guide should provide you with the needed information to appropriately package and ship your samples to us.

All the DNA preparation requirements are included in our DNA sample submission protocol.

Everything you need to know about sending your samples to us is in our Sending Your Samples Guide.

Packaging instructions for biological samples (P650) can be downloaded here.

If you have any additional questions please email us at info@microbesng.com.

Sequencing

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 in a hybrid assembly, to produce improved, and often fully complete and circularised, genome assemblies for bacterial strains

MicrobesNG will soon be launching a New Shotgun Metagenomics Sequencing Service! To find out more please email us at info@microbesng.com.

We do not offer other types of sequencing e.g. 16s rRNA, RNA-seq, ChIP-seq or TraDIS.

No, microbial genomes are much more interesting.

Bioinformatics

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.

New “Bolt On” Bioinformatics services will be coming soon, so watch this space!

In your project portal, you will find the Trimmed reads, the Assemblies and the Taxonomic distribution.

In the Trimmed reads section, when you download your reads there will be four files for each sample:

  1.  samplename_1_trimmed.fastq.gz (forward reads for sample)
  2. samplename_2_trimmed.fastq.gz (reverse reads for sample)
  3. samplename_U1_trimmed.fastq.gz (forward reads that are unpaired, the reverse read was lost during trimming)
  4. samplename_U2_trimmed.fastq.gz (reverse reads that are unpaired, the forward read was lost during trimming).

The data for your Standard service project will be uploaded onto your project web portal and you will receive an email update once it’s made available.

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 to do the DNA extractions in house to ensure the high purity and integrity required for the Oxford Nanopore long read sequencing. We are working on ways to offer our services for higher BSL bacterial strains in the future and if you would like to explore this as an option please email us at info@microbesng.com.

We can accept DNA for the EGS from viruses, phages and plasmids only. This is because these usually have short genomes and usually standard DNA extraction methods produce DNA fragments that are long enough to get good EGS assemblies for these samples. In any case, we will assess the quality of your DNA extractions before you can send us any samples for EGS.

Yes! We can 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.

At the moment, the data for the Enhanced Service is provided through a web link and not through the project portal. However, when the Illumina part of your Enhanced project is completed, we upload that data to your project portal, as many of our customers find this useful. Then when the long read data is available too, you will be sent the web link to access the combined data. We are planning to add more information and include the combined  data in your project portal; this is currently under development.

General

We aim to make the analysed sequenced data available to you within 8-10 weeks of receiving the sample. You can see our live median wait time on our home page. If you have a specific requirement for project completion, let us know and we will see what we can do. Just email us on info@microbesng.com.

The methods document below, covers all services:

MicrobesNG Genome Sequencing Service Methods

In some instances discounts can be applied on higher volume orders. If you would like to enquire about a discount based on the number of samples you plan to send please email us on info@microbesng.com.

OR

If you have sequenced with us and acknowledge MicrobesNG in your publication we will give you 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 or include these directly in the comments section of your next quote request, and we will do the rest: info@microbesng.com

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

If you would like to place an order, please request a quote online.

If you are sequencing strains, we will send you a tube pre loaded with an inactivation buffer for each strain.

Alternatively, for the Standard Service, you can send us extracted DNA (in which case we will  allocate barcode numbers for you to use and not post them out unless specifically requested).

It is your responsibility to put the correct  sample in each tube and return them to us. The tubes will be loaded onto our robot to perform DNA extraction (for strains) and Illumina/ and or ONT library preparation, and they will then be sequenced.  The raw sequence data will be processed using our automated bioinformatic analysis pipeline, and returned to you via your project portal on 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.

Yes, after an extremely successful five years of working within the University of Birmingham our BBSRC grant came to an end and we moved 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.

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 (http://www.microbesng.com) which is supported by the BBSRC (grant number BB/L024209/1).

September 2019 onwards:

Genome sequencing was provided by MicrobesNG (http://www.microbesng.com).


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 “Do you offer discounts?” for details).

Our general pricing can be found on our website's home page. If you would like to request a quote, please fill in our brief online quote request form.

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