Next Generation Sequencing

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

• Create a knowledge sharing platform for bioinformaticians
• Provide easy-to-use NGS software and pipelines for lab scientists
• Build up a nation-wide expert team on Next Generation Sequencing that will serve life science at large

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

• Members -- want to be a member? Please contact Leon Mei.
• Meetings -- regular monthly NGS meetings are open to public, so welcome to join us!
  • Our next meeting will be on December 13th.
  • To receive the announcement of meetings, you could subscribe to the general BioAssist mailing list.

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)	Bioinformatics practices, tips & tricks @LUMC
Illumina MiSeq	Rutger Brouwer (EMC) Alex Bossers (CVI-WUR Lelystad)	MiSeq@CVI-WUR MiSeq@ErasmusMC
LifeTech SOLiD	Victor Guryev (UMCG) Christian Gilissen (UMCN)	SOLiD@UMCN
LifeTech IonTorrent	Yahya Anvar (LUMC)	IonTorrent@LUMC
PacBio	Yahya Anvar (LUMC)	PacBio@LUMC

Activities & Projects

Our task force has been active in the following areas:

• De novo assembly
• Mapping alignment
• SNP/Indel/CNV calling
• Visualization
• Quality Control
• RNA-Seq
• Chip-Seq

See also: A complete list of NGS Projects

Knowledge Base

• Galaxy trainings
• NGS Tools
• Infrastructure/e-Science
• Tips and Tricks
• Mendeley paper sharing site

We are working with NBIC BioWise program on the following courses

• 2011 advanced RNA-seq course
• Leiden bi-yearly NGS 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.