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kSNP3 - find SNPs in DNA sequences and estimate phylogenetic trees

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kSNP3 is a software package to find single nucleotide polymorphisms in DNA sequences and estimate phylogenetic trees. It comes with pre-compiled versions of a number of other programs (Consense, FastTree, Jellyfish, Mummer, Parsimonator and sa).


See the kSNP3_user guide for detailed licensing information and the format for citing the software (requested by the authors) should you choose to use it.

Running kSNP3 on Breezy

Breezy accounts are not set up automatically.  If you don't already have one, see the Breezy QuickStart Guide for instructions on obtaining a Breezy account.

To set up your environment (only the command PATH is modified), use:

module load ksnp/3.021

The kSNP3_user guide indicates that the software has been run on a 48 GB Linux machine without memory issues.  However, actual memory requirements may be considerably less, as they have also run it on a 16 GB Macintosh computer.

When running the software, be sure to specify the -CPU argument to the kSNP3 script, otherwise the software will try to use all 24 cores on the Breezy node assigned to your job. By specifying $PBS_NUM_PPN as the -CPU value, the number of cores used by kSNP3 will match the number requested of the batch job system.  For example, if you include the directives shown below as part of your job script:

#PBS -l mem=40gb
#PBS -l nodes=1:ppn=4

module load ksnp/3.021
kSNP3 -CPU $PBS_NUM_PPN <other arguments>

then, the ppn value specified will be assigned to the environment variable PBS_NUM_PPN and passed on to kSNP3.  The memory and ppn values shown are just examples.  You should tailor the values according to your own experience and data sets.

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2016-09-19 - Created page.

System Breezy
Version 3.021