Soapdenovo2 r240: Difference between revisions

Revision as of 13:45, 15 March 2014

SOAPdenovo2 is a popular genome assembler.

The module file can be found in this location:

 /cm/shared/modulefiles/SHARED/

<source lang='tcl'>#%Module1.0#######################################################################

proc ModulesHelp { } {

       puts stderr "\tAdds SOAPdenovo2 r240 to your environment"

}

module-whatis "Adds SOAPdenovo2 r240 to your environment"

set soapdenovo2_r240_root /cm/shared/apps/SHARED/SOAPdenovo2/SOAPdenovo2-bin-LINUX-generic-r240/

prepend-path PATH $soapdenovo2_r240_root

</source>

The pre-compiled binaries were downloaded from SourceForge on 15-03-2014:

  http://sourceforge.net/projects/soapdenovo2/files/SOAPdenovo2/

This included the GapCloser software (v1.12)

~

@@ Line 1: / Line 1: @@
-'''[http://en.wikipedia.org/wiki/BLAT_(bioinformatics) BLAT]''' (BLAST-like alignment tool) is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC) in the early 2000s to assist in the assembly and annotation of the Human Genome.
+'''[http://soap.genomics.org.cn/soapdenovo.html#intro2 SOAPdenovo2]''' is a popular genome assembler.
@@ Line 26: / Line 26: @@
 == Installation details ==
-The entire suite of binaries/executable was downloaded on 20-12-2013:
+The pre-compiled binaries were downloaded from SourceForge on 15-03-2014:
-<source lang='bash'>
+   http://sourceforge.net/projects/soapdenovo2/files/SOAPdenovo2/
-rsync -aP rsync://hgdownload.cse.ucsc.edu/genome/admin/exe/linux.x86_64/ ./
+This included the GapCloser software (v1.12)
-</source>
 == See also ==
@@ Line 36: / Line 35: @@
 == External links ==
-* [http://genome.ucsc.edu/FAQ/FAQblat.html Blat at UCSC]
+* [http://soap.genomics.org.cn/soapdenovo.html#intro2 SOAPdenovo2 home page]
-* [http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ Download page of 64-bit executables for Linux]
+* [http://sourceforge.net/projects/soapdenovo2/files/SOAPdenovo2/ SourceForge link for SOAPdenovo2]
+* [http://sourceforge.net/projects/soapdenovo2/files/GapCloser/ SourceForge link for GapCloser]
 ~