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:
- The arb project
- The Microbial Genomics Group at the MPI Bremen
- The SILVA database
Course material (7.3.2007):
- Power Point slides
- pdf version of the arb manual (from download.arb-home.de/documentation/arb.ps)
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 Visualization course
Michael Greenacre, 23.04.2018
Script.R updated
Script2.R updated
R Multivariate course
Michael Greenacre, 24.-26.04.2018
Script for Day 1
R Kurs für Späteinsteiger (8/2017 Bremerhaven)
POLMAR R-Course "Programming" (3/2017 Bremerhaven)
DAY 1
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/
Day1-ZIP incl. PPT-PDF
Day2-ZIP incl data
Material for lecture on "Linear algebra in the exploration of climate processes"
(in german)
Motivation analyses (Rahmstorf 2003 d18O-data and El Nino EOF1): sst_d18O.R
Material on Clustering, Mapping, CCA:
- CLUST.R
- LDA: training data, test data, Script
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)...
