Genome Assembly

This is a training project proposal for students

Data sets

Ecoli or salmon fish.

Assemblers

1. IDBA
2. SPAdes
3. Velvet

Steps

1. Download data sets.
2. Trim adaptors and do a quality check
3. The pipeline is divided here. Run each assembler to assemble the data directly or apply digitial normalization to study the effect of digital normalization on genome assembly.
4. Evaluate the assembled genome using quast. Per assembler evaluation and also with digital normalization versus without normalization

More Details

For adapter trimming and quality check, install trimgalore::

conda install -c bioconda trim-galore 

Lets Install Assemblers.

IDBA::

conda install -c bioconda idba 

SPAdes::

conda install -c bioconda spades 

Velvet::

conda install -c bioconda velvet 

Read this paper for more details about digital normalization <http://arxiv.org/abs/1203.4802>__

You will need to install khmer for diginorm ::

conda install -c bioconda khmer 

Finally for evaluation, install Quast ::

conda install -c bioconda quast