NGS Member Overview

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Platform leader: Dr. Roeland van Ham (WUR / CBSG)

Key scientists: Prof. Jack Leunissen (WUR / CBSG), Prof. Edwin Cuppen (Hubrecht Laboratory/CGC), Dr. Johan den Dunnen (LUMC/CMSB), Dr. Wilfred van IJcken (EMC/CGC), Dr. Andrew Stubbs (EMC), Dr. Morris Swertz (UMCG/BBMRI-NL liaison)

Jan van Haarst

Profile on networks:LinkedIn

We are currently busy with de novo assembly of

  • Tomato : Mostly 454 Ti data, plus Sanger reads and a couple of SOLiD runs (in total about 90 Gbase)
  • Potato : Mostly Illumina reads, ranging from 75-125 bp, plus Sanger reads and a few 454 runs.

We have experience with

  • newbler,
  • MIRA
  • SOAPdenovo

At the moment I'm trying to get ABySS, Velvet and EULER-SR to work on the potato set.

  • Programming skills : BASH, PERL and PYTHON.
  • OS : Windows, Linux, OSX

We mostly run the software on our own cluster(s), one of which contains a machine with 256GB.

Matthew Hestand (Former Member)

During my time at the LGTC and NBIC I worked on mainly Helicos/Illumina expression (DeepCAGE/DeepSAGE), (re)sequncing, and ChIP-seq data. General analysis information is at the LGTC webpage. I was also active getting analysis modules into local Galaxy installs and in giving a bi-yearly next-generation sequencing course. My NBIC postion has ended on September 8th and starting mid-November 2010 I will be a post-doc at the University of Kentucky.

Joris Lops

Profile on networks: LinkedIn, myExperiment

Sequence platforms: Illumina.

Software that we use: Molgenis, Galaxy, Hadoop, Illumina pipeline,

Application developed:

  • setup of sequencing pipeline and support for analysis of sequencing data.
  • SequenceLIMS with Morris. Some more info at
  • Maintenance and development of Molgenis
  • Setup sequencing pipeline and assisting with data analysis.
  • Storing genotype/phenotype data for cohort studies (prototype Hadoop as data store).

Programming language / IT platforms:

  • Programming languages: Java
  • Hadoop for storing genotype/phenotype data.

Leon Mei

Leon Mei is the primary contact person in the BioAssist Engineering Team for the sequencing platform.

Profile on networks: LinkedIn[1], myExperiment[2]

I have work experience on software architecture, bio-signal processing, task assignment and scheduling algorithms.

Programming language / IT platforms:

  • Programming languages: Java, C, MySQL, Matlab, PHP
  • Linux, Windows

Barbera van Schaik

Profile on networks: LinkedIn[3], myExperiment[4], Bioinformatics Laboratory at AMC[5]

Sequence platforms: Roche FLX/Titanium, ABI Solid

Software we use: bwa, samtools, varscan, blat (local and on grid), blast (on grid), roche package, celera assembler (cabog), R, Solid RNApipeline, IGV

Sequence applications we (have) work(ed) on:

  • Basic stuff: group sequences per MID, count things, run existing analysis software
  • Splice variant detection
  • Metagenomics (virus discovery)
  • Sequence assembly of bacteria strains
  • Small RNAs
  • Re-sequencing

Programming language / IT platforms:

  • Perl and shell scripting
  • Linux, Dutch grid (EBioInfra[6], VBrowser, Moteur)

Jurgen Nijkamp

Profile on network: LinkedIn[7]

I currently work on a de novo assembly of a yeast strain.

Sequence platforms: Illumina and 454 Software: Maq, Velvet, Nucmer, Lookseq and Abyss

Programming language / IT platforms: Mac OS X / Perl / Matlab / Shell scripting

Victor de Jager

Sequence applications:

  • I am currently working on a metagenomics project involving 1)gut microbiota and 2) a complex starter culture. Focus and expertise on functional diversity, strain and variation detection.
  • Snp/Indel detection and annotation
  • Sequence assembly, (de novo and resequencing) of bacteria
  • Taxonomy determination

Sequence platforms: Roche FLX/Titanium, Illumina Solexa,

Software that we use: blat (local+grid), blast (Local+grid), Roche newbler, Celera WGS Assembler, Soapsnp, Maq, Megan, RDP(Arb), FGweb, Django, GMOD Tools

Software that we develop: Robust SNP/Indel detection & annotation tool (Perl), Metagenomics annotation pipeline Using Grid version of InterproScan, Metagenomics mining tool based on HMMs

Programming language / IT platforms:

  • Programming languages: (Bio)Perl, (Bio)Python , R, Shell scripting, Taverna
  • Databases: PostgreSQL, MySQL
  • Linux, Windows, Mac

Frans Ruzius

I am working on a pipeline for SOLiD sequencing data. We have an in-house SOLiD sequencer and the neighbouring hospital recently bought a SOLiD. Currently I'm testing BWA as a substitute for MAQ and SHRiMP as a alignment tool for color space sequencing data, and also verifying the indels detected by BWA/SAMtools in human and rat. This in combination with tools / filters to validate and detect SNPs and indels.

Programming languages: Perl/CGI/Bash, R, JAVA, C/C++, CUDA, Python, PHP,(Visual) Basic. Data management: MySQL, SGE Linux and Windows

Christian Gilissen

We're working with the Roche/454 Titanium sequencer mainly in combination with enrichment strategies. We use this for gene identification by finding causative mutations in the DNA of (human) patients. We've set up a JAVA pipeline for automated analysis of this kind of data and the prioritization of variants. A second application is the use of these techniques in a diagnostic setting in combination with barcoding.

We also work with a SOLiD sequencer for doing exome enrichment. We're setting up a similar analysis pipeline as for the Roche, in combination with the lifetech Bioscope package.

Programming languages etc.: Java, python, Bash. Torque, mysql, linux and windows.

Experience with: Roche software (newbler), lifetech Bioscope