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

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):

Staden package

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

R is a flexible and powerful open source statistical analysis environment.

Links:

AWI-SAHFOS Summerschool Helgoland 2014

Biodiversity bioinformatics and molecular sequence data

PSeq-Object to loadPCO-tool set to runPresentation-PDF

POLMAR R-Course "Programming" (9/2016 Bremerhaven)
DAY 1
DAY 2

Experiments Day1

Experiments Day2

 

POLMAR R-Course 2013 (POTSDAM)

Clust-2013.R

Material for lecture on "Linear algebra in the exploration of climate processes" 

(in german)

eof-1.R

Motivation analyses (Rahmstorf 2003 d18O-data  and El Nino EOF1): sst_d18O.R

 

Material on Clustering, Mapping, CCA:

Marker saturation

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)...

Download R functions

aflp-simple+MS-dice-plot
aflp.mantel-simple-50reps-to50