Day 1
- Quality Control of Sequence data
- Artemis viewer
Day2
- Mapping sequence data
- Genome Assembly
Day 3
- Genome Annotation
Day 4
- Metagenomics
Instructions
The course website is found here: [http://41.89.129.26/eanbit2020/]
Download the file eanbit2020.tar.gz from the site to your home directory on the server where you want to work.
[wget http://41.89.129.26/eanbit2020/eanbit2020.tar.gz .]
Uncompress the file:
tar zxvf eanbit2020.tar.gz
Change to the eanbit2020 directory and you will see the four folders with the tutorial instructions and data for the course.
Create a new Bioconda environment for the course to install all the necessary software needed for the course using Anaconda.
conda create --name eanbit python=2.7
Activate the newly created eanbit environment:
conda activate eanbit
Install the following packages in the eanbit environment:
conda install -c bioconda fastqc
conda install -c bioconda artemis
conda install -c bioconda trimmomatic
conda install -c bioconda bwa
conda install -c bioconda samtools
conda install -c bioconda bcftools
conda install -c bioconda velvet
conda install -c bioconda blast
conda install -c bioconda ratt
conda install -c bioconda augustus
conda install -c bioconda tophat
conda install -c bioconda cufflinks
conda install -c bioconda gatk
conda install -c hcc abacas