0. Data and software

Data

First, let's check to see how much space you all have in your home directories. Our data download will take up 905 Mb and will expand over the course of the week. If are nearing your quota, please try to delete any unnecessary files.

df -h ~

Course data can be downloaded /bioinf/transfer/marmic_NGS2017. First change to your home directory. Then copy and paste the following command. rsync efficiently transfers and synchronizes files across computer systems.

cd ~
rsync -rv --bwlimit=50000 /bioinf/transfer/marmic_NGS2017 .
du -sh ~/marmic_NGS2017

Course lectures can be downloaded from owncloud:

https://owncloud.mpi-bremen.de/index.php/s/4kNlWHEaJi6bXNS

Software

For the course we are going to use the following tools:

16S rRNA gene analysis

Quality control

FastQC

BBtools

cutadapt

Read merging

BBtools

Oligotyping/MED

MED

rRNA identification

SortMeRNA

SILVAngs

(Meta)genome analysis

Quality control

FastQC

BBtools

Assembly

Megahit

SPAdes

Short-read mapping

BBtools

Annotation

Prodigal

GenDB

JCoast

Binning

metabat

anvi'o

Binning quality assessment

checkM

Protein modeling

Chimera