practices, tips & tricks · practices, tips & tricks ngs bioassist meeting 20-05-2011...
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KEBB - Bioinformatics Laboratory
http://www.bioinformaticslaboratory.nl/
Antoine van Kampen
Aldo
Jongejan
Marcel
Willemsen
Barbera
van Schaik
Department of genome analysis
Frank Baas
New project / experiment
• Researcher contacts sequence lab and bioinformatics lab
• Kick-off meeting: info about the project, how can we collaborate, whenis data expected, estimation about start project
• Antoine assigns someone to the project (Marcel, Aldo, Barbera)
• Weekly meetings: Antoine, Marcel, Aldo, Barbera
• Ad-hoc meetings: biomedicalresearchers with one or two of us
Project management / documentation
• Overview projects and planning: Excel
• Progress, communication, documentation: Twiki
• Track tasks for project: Basecamp
• Hour registration: Kimai / Excel
• Software repository: svn
• No complex project software
• Keep it simple
Analysis
• Do some research on the biological question– Pubmed, Google, Wikipedia, SeqAnswers
• Can he/she do the analysis by his/her self?– Advice
• Is there an existing method?– If so: learn how it works and use it
• Develop new method– Short development cycles
– Take into account to use it in a workflow
• Computation / data intensive?– No: use biolab or seqlab server
– Yes: use grid, cloud, cluster
Projects
T- and B-cell variation
Virus discovery
Alternative splicing
Assembly and comparison bacteria
microRNA expression
Bisulfite sequencing (not yet)
Whole transcriptome bacteria
Chip-seq (only alignment, rest by dep. of Human Genetics)
Exome and whole genome re-sequencing
Genome of the Netherlands
Tools
Existing software
• BLAST
• BLAT
• BWA
• BFAST (testing)
• Annovar
• Varscan
• Newbler
• DEseq
Home made software
• Data format converters
• Quality trimming
• Alternative splice product detection
• CDR3 detection (T- and B-cell variation)
• G-test (Jan Ruijter)
• Genome comparison (small genomes)
• Roche software
• Solid software
• Cabog
• GATK
• Picard
• Samtools
• FastQC
KEBB - Bioinformatics Laboratory
http://www.bioinformaticslaboratory.nl/
Antoine
van Kampen
Silvia
Olabarriaga
Shayan
ShahandMark
Santcroos
Angela
Luyf
Vladimir
Korkhov
Yassene
Mohammed
e-BioInfra architecture
Provided by Shayan Shahand
Workflow technology