Team 2 Report : SOAPdenovo 2

SOAP stands for Short Oligonucleotide Analysis Package

It uses a sparse de Bruijn graph to assemble the genome

It is developed by the Beijing Genomics Institute

One of the unique features of this assembler is that it uses multiple k-mer sizes in order to extract extra information from repeats.

The user supplies a configuration file which contains information on the location and type of data as well parameters which affect the speed and quality of the assembly.

When using Soapdenovo it is important to consider memory requirements as well as the quality of the reads.

Two adapter trimmers were tested, Skewer and AdapterRemoval.

Skewer was faster and easier to use.

Error correction was done with Musket. However, fewer reads were corrected than anticipated.

Kmer analysis done with kmergenie indicated that the optimal kmer size for the de Bruijn graph is 61 bases.