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 and general data analysis environment.

Links:

R Kurs für Späteinsteiger (8/2017 Bremerhaven)

Daten1

Tag 1+2

POLMAR R-Course "Programming" (3/2017 Bremerhaven)
DAY 1

DAY 2

step4.R for multiple-file analyses, see prepmf.R (Day2-ZIP)

 R for Paleo modellers

ZIP ; NetCDFs found on csys-FS or biseqa:/tmp/R-Paleo/

Paleo-src.ZIP

Day1-ZIP incl. PPT-PDF

 Day2-ZIP incl data

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