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DTSTAMP:20260614T153539Z
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DTSTART:20210526T030000Z
DTEND:20210526T070000Z
DESCRIPTION:The analysis of a viral genome and its variants has unique chal
 lenges\, most notably the inability to culture the virus outside of the ho
 st organism. Furthermore\, many viruses have a high mutational rate which\
 , coupled with the culturing restrictions\, make determining viral variant
 s more of a heterogeneous population exercise.\n\nIn this online workshop 
 we focus on the tools and workflows available for variant calling in virus
 es in Galaxy Australia. During the workshop you will get hands-on experien
 ce using BWA-MEM for alignment\, lofreq for variant calling and SnpEff for
  annotating variant effects. The workshop makes use of COVID-19 variant ca
 lling data however the tools and workflows are equally applicable to other
  viruses and biological questions.\n\nAccess to all of the tools covered i
 n this workshop is via [Galaxy Australia](https://usegalaxy.org.au/)\, an 
 online platform for biological research that allows people to use computat
 ional data analysis tools and workflows without the need for programming e
 xperience.\n\n\nYou may also be interested in our workshops on variant cal
 ling in polyploid organisms (e.g. humans\, plants and animals) and bacteri
 a. See our [events page](https://www.biocommons.org.au/events) for more in
 formation.\n\n\n**Date/time**: 1-5pm AEST\, Wednesday 26 May 2021\n\n\n**L
 ead Trainers:**  Dr Gareth Price\, Dr Igor Makunin\, QCIF Bioinformatics.\
 n\n\n**Learning outcomes**\n\n\nThe materials to be covered in the worksho
 p are freely available via the [Galaxy Training Network](https://training.
 galaxyproject.org/training-material/topics/variant-analysis/tutorials/sars
 -cov-2/tutorial.html).\n\n\nBy the end of the workshop you should be able 
 to:\n\n- Download and import reference genome data\n- Align reads using BW
 A-MEM\n- Call variants using lofreq\n- Annotate variant effects with SnpEf
 f\n\nThe workshop will NOT provide an introduction to the basics of Galaxy
  or the use of Galaxy for sequencing analysis (e.g. quality control and ma
 pping). If you would like to learn about these topics there are several tu
 torials available via the [Galaxy Training Network](https://training.galax
 yproject.org/training-material/).\n\n\n**Who the workshop is for**\n\n\nTh
 is workshop is for Australian researchers who have or will work on variant
  calling in viruses as part of their projects.\n\n\nTo get the most out of
  the workshops you must be familiar with the concepts of variant calling a
 nd have some experience with the basics of using Galaxy Australia such as 
 setting up a history\, uploading data and running tools. No programming ex
 perience is required.\n\n\nYou will be required to watch an introductory w
 ebinar (either live or recorded) that will provide an overview of Galaxy A
 ustralia and introduce key functionalities of the service. If you are new 
 to Galaxy we recommend that you work through the following tutorials in ad
 vance: [A short introduction to Galaxy](https://training.galaxyproject.org
 /training-material/topics/introduction/tutorials/galaxy-intro-short/tutori
 al.html) and [Galaxy 101 for Everyone](https://training.galaxyproject.org/
 training-material/topics/introduction/tutorials/galaxy-intro-101-everyone/
 tutorial.html).\n\n\n**How to apply**\n\n\nThis workshop is free but parti
 cipation is subject to application with selection. **_Applications close a
 t 5pm AEST Wednesday 12 May 2021._**\n\n\nYou must be associated with an A
 ustralian organisation and provide an appropriate organisational email add
 ress for your application to be considered.\n\n\nApplications will be revi
 ewed by the organising committee and all applicants will be informed of th
 e status of their application (successful\, waiting list\, unsuccessful) b
 y Friday 14 May 2021. Successful applicants will be provided with a Zoom m
 eeting link closer to the date.\n\n\n**[Apply here](https://biocommons-var
 iants-viruses.eventbrite.com.au/)**\n\n\nThis workshop is presented by the
  [Australian BioCommons](https://www.biocommons.org.au/) and [Queensland C
 yber Infrastructure Foundation (QCIF)](https://www.qcif.edu.au/) with the 
 assistance of a network of facilitators from the national [Bioinformatics 
 Training Cooperative](https://www.biocommons.org.au/training-cooperative) 
 and [Galaxy Australia](https://usegalaxy.org.au/).\n\n\nThis event is part
  of a series of [bioinformatics training events](https://www.biocommons.or
 g.au/events). If you'd like to hear when registrations open for other even
 ts\, please [subscribe](https://www.biocommons.org.au/subscribe) to Austra
 lian BioCommons.
SUMMARY:WORKSHOP: Viral variant calling with Galaxy
URL;VALUE=URI:https://www.biocommons.org.au/events/variants-viruses
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