Monthly Archives: October 2016

Bacteriophage genome assembly and annotation workshop

We will be running a bacteriophage genome assembly and annotation workshop at WMS on Monday 9th of January.  The course will be run on CLIMB  virtual machines, so please register for an account in advance.

Details

Date: Monday 9th January 2017

Cost: £50

Registration and payment by Monday 5th December* – registration form is open – here

Spaces: 20


Overview

Attendees may provide up to four samples of bacteriophage DNA (by 5th Dec 2016) in advance of the workshop, which will be sequenced and the data available for analysis on the 9th of Jan. During the workshop attendees will learn how to quality control their data, assemble bacteriophage genomes, annotate and prepare their genome in a format for submission to EBI.

Registration is on a first come first served basis, so register early. Spaces are limited to 20 people

MRC CLIMB infrastructure will be used for the workshop.


Prior experience:

No prior experience of genome annotation is needed.


Computing/analysis:

Analysis will be run on CLIMB. Users are encouraged to bring their own laptop – a limited number of laptops are available.

A free CLIMB account is also needed. Register here


DNA samples

DNA samples must be received by Monday 5th December for them to be sequenced in time for the course. It is not necessary to send phage samples to attend the course. The workshop is a genome annotation training workshop- sequencing of isolates is a bonus so that attendees can annotate their own genomes.

DNA samples must be sent in a 96 well plate. A minimum of 10 ul of DNA at 10 ng /ul DNA is required. Larger volumes are fine, but must be at concentration of 10 ng / ul.

DNA must be column purified prior to sending, Zymo DNA purification/columns are recommended. Concentration must be determined by use of fluorescent detection system (eg Qubit), not Nanodrop .

Phage do not have to be CsCl purified prior to DNA extraction. The method we use for extraction can be found here https://peerj.com/articles/2055/ , then run through a DNA clean-up column

Please contact Andrew Millard on a.d.millard@warwick.ac.uk after registration, prior to sending any samples. DO NOT JUST SEND SAMPLES

  1. Contact a.d.millard@warwick.ac.uk prior to sending
  2. Label the plate so that your name can be read on the side of the plate.
  3. Complete the form that will be sent when you contact a.d.millard@warwick.ac.uk
  4. Sample names are to be alphanumeric only.