====== Team 2 Report : SOAPdenovo 2 ======
===== Outline =====
  * 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.
===== Using Soapdenovo =====
  * 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.
===== Read assessment  =====
  * 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.