Difference between revisions of "Next Generation Sequencing"

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'''Next generation sequencing''' (or High throughput sequencing) is one of the task forces of [[BioAssist]].
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'''Next generation sequencing''' (or High Throughput Sequencing, Genomics) is one of the task forces of [[BioAssist]].
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For any question regarding this task force, you may contact [[User:Leon|Leon Mei]].
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== Main Missions ==
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* '''''Create a [[Next Generation Sequencing: Meetings|knowledge sharing platform]] for bioinformaticians'''''
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* '''''Provide easy-to-use [[NBIC Galaxy Server: NBIC Pipelines |NGS software and pipelines]] for lab scientists'''''
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* '''''Build up a nation-wide [[NGS Member Overview|expert team]] on Next Generation Sequencing that will serve life science at large'''''
  
 
== Recent Highlights ==
 
== Recent Highlights ==
* 19-11-2010, a small group was formed to work on standardizing QC and eventually a QC pipeline in NBIC Galaxy: Jan van Haarst, Frans-Paul Ruzius, Jeroen Laros, Wil Koetsier, Victor de Jager (coordinator).
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* On June 18th, 2013, a taskforce PI meeting was successfully held. Report can be found at [http://www.nbic.nl/about-nbic/news-press/bioinformatics-news/detail/article/bioassist-ngs-pi-meeting-past-june-18th/ the NBIC news site].
* 15-11-2010, the first test version of NBIC [[Galaxy VM]] is released! Direct download link [[http://bet1.nbiceng.net/galaxy/ here]
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* 4-11-2010, our task force had a major contribution to the [http://www.medgencentre.nl/ MGC course: Next Generation Sequencing (NGS) data analysis course] in Leiden.
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* 15-10-2010, kickoff the development on the advanced simulated dataset generation script. The involved members are Frans-Paul Ruzius, Kai Ye, Victor de Jager, Victor Guryev, Rutger Brouwer, and Leon Mei.
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* 5-10-2010, Joint force on [http://bbmri.nl/nl-nl/activiteiten/projecten/98-het-genoom-van-nederland GvNL] between the BBMRI project and our NGS task force. The involved members are Freerk van Dijk, Barbera van Schaik, Jeroen Laros, Kai Ye, and Leon Mei.
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[[Next Generation Sequencing: Recent Highlights | more highlights]]
 
[[Next Generation Sequencing: Recent Highlights | more highlights]]
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== General Information ==
 
== General Information ==
 
* [[NGS Member Overview|Members]] -- want to be a member? Please contact [[User:Leon|Leon Mei]].
 
* [[NGS Member Overview|Members]] -- want to be a member? Please contact [[User:Leon|Leon Mei]].
* [[Next Generation Sequencing: Meetings|Meetings]] -- regular monthly NGS meetings are open to public, so welcome to join us!
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* [[Next Generation Sequencing: Meetings|Meetings]] -- regular monthly NGS meetings are open to public, so welcome to join us!  
* [[Next Generation Sequencing: Inventory|Inventory]] -- an overview of machines, tools, and data storage formats used by the member groups.
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** Our next meeting will be on [[NGS_Meeting_on_13-12-2013|December 13th]].
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** To receive the announcement of meetings, you could subscribe to  [https://horus.sara.nl/mailman/listinfo/bioassist-users the general BioAssist mailing list].
  
== Activities ==
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You can visit the Netherlands part of [http://pathogenomics.bham.ac.uk/hts/ the world map of sequencers] to see who are running what.
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Here are a brief summary of our experts on different sequencing technology.
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{| cNamelass="wikitable sortable" border="1"
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|-
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! Platform
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! Data Expert
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! Presentations/Tutorial
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|-
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| Illumina HiSeq
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|
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* Rutger Brouwer (EMC)
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* Jeroen Laros (LUMC)
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* Freerk van Dijk (UMCG)
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* Kai Ye (former LUMC)
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|
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* [[Media:JLaros_Bioinf_practice_Utrecht_15_07_11.pdf‎ |Bioinformatics practices, tips & tricks @LUMC]]
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|-
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| Illumina MiSeq
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|
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* Rutger Brouwer (EMC)
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* Alex Bossers (CVI-WUR Lelystad)
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|
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* [[Media: 20120913_Nbic_Bossers_MiSeqApps_v08.pdf| MiSeq@CVI-WUR]]
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* [[Media: Rutger_2012-6-22.pdf | MiSeq@ErasmusMC]]
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|-
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| LifeTech SOLiD
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|
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* Victor Guryev (UMCG)
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* Christian Gilissen (UMCN)
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|
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* [[Media:NGS Christian Gilissen 2010 6 11.pdf | SOLiD@UMCN]]
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|-
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| LifeTech IonTorrent
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|
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* Yahya Anvar (LUMC)
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|
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* [[Media: Yahya_2012-10-12.pdf|IonTorrent@LUMC]]
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|-
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| PacBio
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|
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* Yahya Anvar (LUMC) 
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|
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* [[Media: Yahya_2012-05-25.pdf |PacBio@LUMC]]
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|-
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|}
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== Activities & Projects ==
 
Our task force has been active in the following '''areas''':
 
Our task force has been active in the following '''areas''':
 
* [[NGS De Novo Assembly Expertise | De novo assembly]]
 
* [[NGS De Novo Assembly Expertise | De novo assembly]]
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* [[NGS Visualization Expertise | Visualization]]
 
* [[NGS Visualization Expertise | Visualization]]
 
* [[NGS Quality Control | Quality Control]]
 
* [[NGS Quality Control | Quality Control]]
 
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* [[NGS RNA-Seq | RNA-Seq]]
And here are a few '''projects''' that we are working on:
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* [[NGS Chip-Seq | Chip-Seq]]
* [[Benchmarking Alignment & Variants Calling Software | Benchmarking alignment software]]  
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* [[Simulated Dataset Generation Script | Simulated dataset generation script]]
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* [[Benchmarking De Novo Assembly Software| Benchmarking de novo assembly software]]
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* [[NBIC Galaxy Server: NBIC Pipelines | Shared NGS pipelines]]
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* [[NBIC Galaxy Server|NBIC Galaxy Server]]
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* [[GvNL|"Het Genoom van Nederland"]]
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See also: A complete list of [[:Category:Next Generation Sequencing / Project|NGS Projects]]
 
See also: A complete list of [[:Category:Next Generation Sequencing / Project|NGS Projects]]
  
 
== Knowledge Base ==
 
== Knowledge Base ==
Here are additional NGS related knowledge that are collected by our task force (in particular [[User:Marcvandriel | Dr. Marc van Driel]]). They are from mixed sources like pubmed, tool websites, [http://seqanswers.com seqanswers.com], etc.
 
  
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* [[Galaxy trainings]]
 
* [[NGS Tools]]  
 
* [[NGS Tools]]  
* [[NGS File Format]]
 
 
* [[Next Generation Sequencing: Infrastructure|Infrastructure/e-Science]]
 
* [[Next Generation Sequencing: Infrastructure|Infrastructure/e-Science]]
* [[Next Generation Sequencing: Data sources|Data sources]]
 
* [[Next Generation Sequencing: Instrumentation|Instrumentation]]
 
* [[Next Generation Sequencing: Other related companies|Other related companies]]
 
 
* [[Next Generation Sequencing: TipsTricks| Tips and Tricks]]
 
* [[Next Generation Sequencing: TipsTricks| Tips and Tricks]]
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* [http://www.mendeley.com/groups/1780271/ngs-bioassist/ Mendeley paper sharing site]
  
== Upcoming Events ==
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We are working with NBIC BioWise program on the following courses
 
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* [[2011 advanced RNA-seq course]]
* January 21st, 2011, 9:00-12:00, [[Agenda BioAssist Programmers Meeting 2011/1/21 | RNA-seq seminar]]. SURF Utrecht.
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* Leiden bi-yearly NGS courses
* November 14th&15th, 2011, [http://www.nextgenerationsequencing-congress.com/index.asp Next Generation Sequencing Congress], Radisson Edwardian, Heathrow, London UK
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== Copyright ==
 
== Copyright ==
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[[Category:Next Generation Sequencing]]
 
[[Category:Next Generation Sequencing]]
 
For any question regarding this platform, you may contact [[User:Leon|Leon Mei]].
 

Latest revision as of 09:27, 20 January 2016

Next generation sequencing (or High Throughput Sequencing, Genomics) is one of the task forces of BioAssist.

For any question regarding this task force, you may contact Leon Mei.

Main Missions

Recent Highlights

  • On June 18th, 2013, a taskforce PI meeting was successfully held. Report can be found at the NBIC news site.

more highlights

General Information

You can visit the Netherlands part of the world map of sequencers to see who are running what.

Here are a brief summary of our experts on different sequencing technology.

Platform Data Expert Presentations/Tutorial
Illumina HiSeq
  • Rutger Brouwer (EMC)
  • Jeroen Laros (LUMC)
  • Freerk van Dijk (UMCG)
  • Kai Ye (former LUMC)
Illumina MiSeq
  • Rutger Brouwer (EMC)
  • Alex Bossers (CVI-WUR Lelystad)
LifeTech SOLiD
  • Victor Guryev (UMCG)
  • Christian Gilissen (UMCN)
LifeTech IonTorrent
  • Yahya Anvar (LUMC)
PacBio
  • Yahya Anvar (LUMC)

Activities & Projects

Our task force has been active in the following areas:

See also: A complete list of NGS Projects

Knowledge Base

We are working with NBIC BioWise program on the following courses

Copyright

Information that is created on this site is within the public domain. Public domain information on this website may be freely distributed and copied. However, it is requested that in any subsequent use of this work, NBIC is given appropriate acknowledgment.