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lecture_notes:04-22-2015

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.
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lecture_notes/04-22-2015.txt · Last modified: 2015/04/22 16:01 by chkcole