SOAPsnp is a member of the SOAP (Short Oligonucleotide Analysis Package). Despite its name, the program is a resequencing utility that can assemble consensus sequence for the genome of a newly sequenced individual based on the alignment of the raw sequencing reads on the known reference.
See which versions of SOAPsnp are available:
$ module avail SOAPsnp
Load a version of SOAPsnp into your environment and run it:
$ module load SOAPsnp/1.03 $ soapsnp
Notes from the sysadmin during installation:
$ wget http://soap.genomics.org.cn/down/SOAPsnp-v1.03.tar.gz $ tar xf SOAPsnp-v1.03.tar.gz $ cd SOAPsnpZ $ make $ sudo mkdir -p /export/apps/SOAPsnp/1.03/bin $ sudo cp soapsnp /export/apps/SOAPsnp/1.03/bin $ sudo cp COPYING readme release /export/apps/SOAPsnp/1.03