Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection. Parsnp was designed to work in tandem with Gingr, a flexible platform for visualizing genome alignments and phylogenetic trees; both Parsnp and Gingr form part of the Harvest suite :

• Harvest project page
  • url: http://harvest.readthedocs.org

Installation

From conda

Parsnp is available on the Bioconda channel. This is the recommended method of installation. Once you have added the Bioconda channel to your conda environment, parsnp can be installed via

conda install parsnp

From source

To build Parsnp from source, users must have automake 1.15, autoconf, and libtool installed. Parsnp also requires RaxML, Phipack, Harvest-tools, and numpy. Some additional features require Mash, FastANI and FastTree. All of these packages are available via Conda (many on the Bioconda channel).

Build instructions

First, you must build the Muscle library

cd muscle
./autogen.sh
./configure --prefix=$PWD CXXFLAGS='-fopenmp'
make install

Now we can build Parsnp

cd ..
./autogen.sh
./configure
make LDADD=-lMUSCLE-3.7 
make install

If you wish to be able to move your Parsnp installation around after building, build the parsp binary as follows (after building the Muscle library)

./autogen.sh
export ORIGIN=\$ORIGIN
./configure LDFLAGS='-Wl,-rpath,$$ORIGIN/../muscle/lib'
make LDADD=-lMUSCLE-3.7 
make install

Note that the parsnp executable in bin/ is not the same as the one in the root level. The former is an alias for Parsnp.py while the latter is the core algorithm of Parsnp that we build above.

OSX Users (Catalina)

Recent OSX have a Gatekeeper, that's designed to ensure that only softwre from known developers runs on tour Mac. Please refer to this link to enable the binaries shipped with Parsnp to run: https://support.apple.com/en-us/HT202491

Running Parsnp

Parsnp can be run multiple ways, but the most common is with a set of genomes and a reference.

parsnp -g <reference_genbank> -d <genomes> 

parsnp -r <reference_fasta> -d <genomes> 

For example,

./parsnp -g examples/mers_virus/ref/England1.gbk -d examples/mers_virus/genomes/*.fna -c

More examples can be found in the readthedocs tutorial

Misc

CITATION provides details on how to cite Parsnp.

LICENSE provides licensing information.