Benchmarking: SOAPdenovo (Bioinformatics: De novo assembly)

SOAPdenovo

• SOAPdenovo: (SOAP) Short Oligonucleotide Analysis Package
• Homepage: http://soap.genomics.org.cn/index.html

SOAP has been in evolution from a single alignment tool to a tool package that provides full solution to next generation sequencing data analysis. Currently, it consists of a new alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder ( SOAPindel ), a structural variation scanner ( SOAPsv ) and a de novo short reads assembler ( SOAPdenovo ). And a GPU-accelerated alignment tool (SOAP3/GPU) are being implemented.

Build

• Get the source from: http://sourceforge.net/projects/soapdenovo2/files/?source=navbar
• Version 233

  # Version 233 built with openCC/opencc 4.5.2.1
  tar zxvf SOAPdenovo2-src-r223.tgz
  cd r233/sparsePregraph
  # edit the Makefile, set CC=openCC
  make
  cd ../standardPregraph
  # edit the Makefile, set CC=opencc
  make 
  make 127mer=1

• Version 240

  # Version 240 built with openCC/opencc 4.5.2.1
  tar zxvf SOAPdenovo2-src-r240.tgz
  cd SOAPdenovo2-src-r240
  # edit Makefile, set CC=openCC
  # edit sparsePregraph/Makefile, set CC=openCC
  # edit standardPregraph/Makefile, set CC=opencc
  make

Run Analysis

• example.config; take this file from the SOAPdenovo home page

Notes on Bioinformatics

Good summary of Bioinformatics computational demands here: http://www.biogrid.jp/pdf/jsbicbi2012.pdf

Computational requirements for the different types of Analysis

Pairwise sequence alignment

• Embarrassingly parallel with no communication
• Batches of reads run on different nodes using threading within a node

De novo assembly

• Large shared memory needed in a single node
• More memory needed for reads with more errors
• Threading available

Phylogenetic tree inference

• Parallelization available at fine- and coarse-grain levels
• Hybrid parallel approach using MPI and Pthreads in single RAxML job
• Alternatively, multiple threaded jobs using RAxML-Light

Database search & retrieval

• Can benefit from using flash memory instead of disk

Applications used for different Analysis types

Pairwise sequence alignment

• ATAC, BFAST, BLAST, BLAT, Bowtie, BWA

Multiple sequence alignment (via CIPRES gateway)

• ClustalW, MAFFT

RNA-Seq analysis

• TopHat, Cufflinks

De novo assembly

• ABySS, SOAPdenovo, Velvet

Phylogenetic tree inference (via CIPRES gateway)

• BEAST with BEAGLE, GARLI, MrBayes, RAxML, RAxML-Light

Toolkits

• BEDTools, GATK, SAMtools

Database search & retrieval

• IntegromeDB