Benchmarking: SOAPdenovo (Bioinformatics: De novo assembly) - Revision history

David at 20:02, 28 July 2013

2013-07-28T20:02:58Z

David at 14:30, 28 July 2013

2013-07-28T14:30:42Z

David: Created page with "== SOAPdenovo == * SOAPdenovo: (SOAP) Short Oligonucleotide Analysis Package * Homepage: http://soap.genomics.org.cn/index.html SOAP has been in evolution from a single align..."

2013-07-28T14:28:47Z

Created page with "== SOAPdenovo == * SOAPdenovo: (SOAP) Short Oligonucleotide Analysis Package * Homepage: http://soap.genomics.org.cn/index.html SOAP has been in evolution from a single align..."

New page

== 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
<syntaxhighlight>
# 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
</syntaxhighlight>

* Version 240
<syntaxhighlight>

</syntaxhighlight>
== 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

← Older revision		Revision as of 14:30, 28 July 2013
Line 46:		Line 46:
	'''Database search & retrieval'''		'''Database search & retrieval'''
	* Can beneﬁt from using ﬂash memory instead of disk		* 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

@@ Line 9: / Line 9: @@
 * Version 233
 <syntaxhighlight>
-   # Version 233 built with openCC 4.5.2.1
+   # Version 233 built with openCC/opencc 4.5.2.1
    tar zxvf SOAPdenovo2-src-r223.tgz
    cd r233/sparsePregraph
@@ Line 22: / Line 22: @@
 * Version 240
 <syntaxhighlight>
-</syntaxhighlight>
+== Run Analysis ==
 == Notes on Bioinformatics ==
 Good summary of Bioinformatics computational demands here: http://www.biogrid.jp/pdf/jsbicbi2012.pdf