Next Generation Sequencing - Data Analysis
We provide support/services for sequence assembly, mapping (e.g., Illumina on 454 transcriptomes), contig annotation, cluster-analysis, phylogenenetic placement, metagenome / -transcriptome functional comparative analysis, ...
arb is a software environment primarily for ribosomal DNA sequence data, used by several working groups at the AWI. The bioinformatics group provides a platform and user support concerning arb.
Some arb links:
Course material (7.3.2007):
The Staden package is a modular sequence analysis system, originally aimed at assembling genomic contigs. Due to its flexibility, it is used for several other tasks as well. Below is the material from our Staden introduction 2006.
R is a flexible and powerful open source statistical analysis environment.
AWI-SAHFOS Summerschool Helgoland 2014
Biodiversity bioinformatics and molecular sequence data
PSeq-Object to loadPCO-tool set to runPresentation-PDF
POLMAR R-Course "Programming" (3/2015 Bremerhaven)
Day 1 ZIP
Day 2 ZIP
Material on Clustering, Mapping, CCA:
R functions for testing genetic marker (AFLP or microsatellite) saturation for the following paper:
Alpermann, John, Tillmann, Beszteri & Cembella: Population characteristics of Alexandrium tamarense (Dinophyta)...