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| [](https://travis-ci.org/sanger-pathogens/snp-sites) | ||
| # SNP-sites | ||
| Rapidly extracts SNPs from a multi-FASTA alignment. | ||
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| [](https://travis-ci.org/sanger-pathogens/snp-sites) | ||
| [](https://github.com/sanger-pathogens/snp-sites/blob/master/LICENSE) | ||
| [](http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000056) | ||
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| ## Contents | ||
| * [Introduction](#introduction) | ||
| * [Installation](#installation) | ||
| * [Linux \- Ubuntu/Debian](#linux---ubuntudebian) | ||
| * [OSX/Linux \- using Bioconda](#osxlinux---using-bioconda) | ||
| * [OSX/Linux \- from source](#osxlinux---from-source) | ||
| * [OSX/Linux \- from a release tarball](#osxlinux---from-a-release-tarball) | ||
| * [All platforms \- Docker](#all-platforms---docker) | ||
| * [Usage](#usage) | ||
| * [Example input](#example-input) | ||
| * [Example usage](#example-usage) | ||
| * [Output](#output) | ||
| * [License](#license) | ||
| * [Feedback/Issues](#feedbackissues) | ||
| * [Citation](#citation) | ||
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| ## Introduction | ||
| Rapidly decreasing genome sequencing costs have led to a proportionate increase in the number of samples used in prokaryotic population studies. Extracting single nucleotide polymorphisms (SNPs) from a large whole genome alignment is now a routine task, but existing tools have failed to scale efficiently with the increased size of studies. These tools are slow, memory inefficient and are installed through non-standard procedures. We present SNP-sites which can rapidly extract SNPs from a multi-FASTA alignment using modest resources and can output results in multiple formats for downstream analysis. SNPs can be extracted from a 8.3 GB alignment file (1,842 taxa, 22,618 sites) in 267 seconds using 59 MB of RAM and 1 CPU core, making it feasible to run on modest computers. It is easy to install through the Debian and Homebrew package managers, and has been successfully tested on more than 20 operating systems. SNP-sites is implemented in C and is available under the open source license GNU GPL version 3. | ||
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| The software can be cited as: | ||
| ## Installation | ||
| There are a few ways to install SNP-sites. The simpliest way is using apt (Debian/Ubuntu) or Conda. If you encounter an issue when installing SNP-sites please contact your local system administrator. If you encounter a bug please log it [here](https://github.com/sanger-pathogens/snp-sites/issues) or email us at [email protected] | ||
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| * Linux - Ubuntu/Debian | ||
| * OSX/Linux - using Bioconda | ||
| * OSX/Linux - from source | ||
| * OSX/Linux - from a release tarball | ||
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| ["SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments", Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris, Microbial Genomics 2(4), (2016)](http://dx.doi.org/10.1099/mgen.0.000056) | ||
| ### Linux - Ubuntu/Debian | ||
| If you have a recent version of Ubuntu or Debian then you can install it using apt. | ||
| ``` | ||
| apt-get install snp-sites | ||
| ``` | ||
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| ### OSX/Linux - using Bioconda | ||
| Install Conda and install the bioconda channels. | ||
| ``` | ||
| conda config --add channels conda-forge | ||
| conda config --add channels defaults | ||
| conda config --add channels r | ||
| conda config --add channels bioconda | ||
| conda install snp-sites | ||
| ``` | ||
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| ### OSX/Linux - from source | ||
| This is a difficult method and is only suitable for someone with advanced unix skills. No support is provided with this method, since you have advanced unix skills. Please consider using Conda instead. First install a standard development environment (e.g. gcc, automa\ | ||
| ke, autoconf, libtool). Download the software from [GitHub](https://github.com/sanger-pathogens/snp-sites). | ||
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| ``` | ||
| autoreconf -i -f | ||
| ./configure | ||
| make | ||
| sudo make install | ||
| ``` | ||
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||
| ### OSX/Linux - from a release tarball | ||
| This is a difficult method and is only suitable for someone with advanced unix skills. No support is provided with this method, since you have advanced unix skills. Please consider using Conda instead. First install a standard development environment (e.g. gcc, automa\ | ||
| ke, autoconf, libtool). | ||
|
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||
| ``` | ||
| tar xzvf snp-sites-x.y.z.tar.gz | ||
| cd snp-sites-x.y.z | ||
| ./configure | ||
| make | ||
| sudo make install | ||
| ``` | ||
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| ### All platforms - Docker | ||
| Bioconda produce a Docker container so you can use the software out of the box. Install Docker and then pull the container from Bioconda https://quay.io/repository/biocontainers/snp-sites | ||
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| ## Usage | ||
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| ``` | ||
| Usage: snp-sites [-mvph] [-o output_filename] <file> | ||
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@@ -51,60 +121,20 @@ AGT | |
| snp-sites my_alignment.aln | ||
| snp-sites my_gzipped_alignment.aln.gz | ||
| ``` | ||
| ### Output | ||
| * Multi Fasta Alignment - Similar to the input file but just containing the SNP sites. | ||
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| ### Multi Fasta Alignment | ||
| Similar to the input file but just containing the SNP sites. | ||
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| ### VCF | ||
| This contains the position of each SNP in the reference sequence, and the occurrence in each other sample. Can be loaded into Artemis for visualisation. | ||
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| ### Relaxed Phylip format | ||
| All the SNP sites in a format for RAxML and other tree building applications. | ||
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||
| # Installation | ||
| There are a few ways to install snp-sites. The simpliest way is using apt (Debian/Ubuntu) or Conda. | ||
|
|
||
| * Linux - Ubuntu/Debian | ||
| * OSX/Linux - using Bioconda | ||
| * OSX/Linux - from source | ||
| * OSX/Linux - from a release tarball | ||
|
|
||
| ## Linux - Ubuntu/Debian | ||
| If you have a recent version of Ubuntu or Debian then you can install it using apt. | ||
| ``` | ||
| apt-get install snp-sites | ||
| ``` | ||
|
|
||
| ## OSX/Linux - using Bioconda | ||
| Install Conda and install the bioconda channels. | ||
| ``` | ||
| conda config --add channels conda-forge | ||
| conda config --add channels defaults | ||
| conda config --add channels r | ||
| conda config --add channels bioconda | ||
| conda install snp-sites | ||
| ``` | ||
| * VCF - This contains the position of each SNP in the reference sequence, and the occurrence in each other sample. Can be loaded into Artemis for visualisation. | ||
|
|
||
| ## OSX/Linux - from source | ||
| This is a difficult method and is only suitable for someone with advanced unix skills. No support is provided with this method, since you have advanced unix skills. Please consider using Conda instead. First install a standard development environment (e.g. gcc, automake, autoconf, libtool). Download the software from [GitHub](https://github.com/sanger-pathogens/snp-sites). | ||
| * Relaxed Phylip format - All the SNP sites in a format for RAxML and other tree building applications. | ||
|
|
||
| ``` | ||
| autoreconf -i -f | ||
| ./configure | ||
| make | ||
| sudo make install | ||
| ``` | ||
| ## License | ||
| SNP-sites is free software, licensed under [GPLv3](https://github.com/sanger-pathogens/snp-sites/blob/master/LICENSE). | ||
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| ## OSX/Linux - from a release tarball | ||
| This is a difficult method and is only suitable for someone with advanced unix skills. No support is provided with this method, since you have advanced unix skills. Please consider using Conda instead. First install a standard development environment (e.g. gcc, automake, autoconf, libtool). | ||
| ## Feedback/Issues | ||
| Please report any issues to the [issues page](https://github.com/sanger-pathogens/snp-sites/issues) or email [email protected] | ||
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||
| ``` | ||
| tar xzvf snp-sites-x.y.z.tar.gz | ||
| cd snp-sites-x.y.z | ||
| ./configure | ||
| make | ||
| sudo make install | ||
| ``` | ||
| ## Citation | ||
| If you use this software please cite: | ||
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| ## All platforms - Docker | ||
| Bioconda produce a Docker container so you can use the software out of the box. Install Docker and then pull the container from Bioconda https://quay.io/repository/biocontainers/snp-sites | ||
| "SNP-sites: rapid efficient extraction of SNPs from multi-FASTA alignments", Andrew J. Page, Ben Taylor, Aidan J. Delaney, Jorge Soares, Torsten Seemann, Jacqueline A. Keane, Simon R. Harris, [Microbial Genomics 2(4), (2016)](http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000056) | ||