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 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

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