SKA (Split Kmer Analysis) is a toolkit for prokaryotic (and any other small, haploid) DNA sequence analysis using split kmers. A split kmer is a pair of kmers in a DNA sequence that are separated by a single base. Split kmers allow rapid comparison and alignment of small genomes, and is particulalry suited for surveillance or outbreak investigation. SKA can produce split kmer files from fasta format assemblies or directly from fastq format read sequences, cluster them, align them with or without a reference sequence and provide various comparison and summary statistics. Currently all testing has been carried out on high-quality Illumina read data, so results for other platforms may vary.
Installation
Installation using Conda
conda install -c bioconda ska
Many thanks to John Lees for creating this Conda recipe!
Installation using Homebrew
brew install brewsci/bio/ska
Many thanks to Torsten Seemann for creating this Brew formula!
Installation from source
SKA can be installed by cloning this repository and running make
git clone https://github.com/simonrharris/SKA
Or by Downloading and unpacking the latest release.
Then simply navigate into the SKA directory and run make
cd SKA
make
The executable will be compiled into a directory named bin. You can either add this bin directory to your path or move the executable into a path directory.
sudo make install
will move the executable to /usr/local/bin.
Requirements
SKA simply requires GNU make and a version of g++ which supports C++11.
Usage
ska <subcommand>
Subcommands:
align Reference-free alignment from a set of split kmer files
alleles Create a merged split kmer file for all sequenes in one or
more multifasta files
annotate Locate/annotate split kmers in a reference fasta/gff file
compare Print comparison statistics for a query split kmer file
against a set of subject split kmer files
distance Pairwise distance calculation and clustering from split kmer
files
fasta Create a split kmer file from fasta file(s)
fastq Create a split kmer file from fastq file(s)
humanise Print kmers from a split kmer file in human readable format
info Print some information about one or more kmer files
map Align split kmer file(s) against a reference fasta file
merge Merge split kmer file(s) into one file
summary Print split kmer file summary statistics
type Type split kmer files using a set of allele files
unique Output kmers unique to a set of split kmer files
version Print the version and citation for ska
weed Weed kmers from a split kmer file
Please read the SKA wiki page for full usage instructions.
Contents
Introduction
SKA (Split Kmer Analysis) is a toolkit for prokaryotic (and any other small, haploid) DNA sequence analysis using split kmers. A split kmer is a pair of kmers in a DNA sequence that are separated by a single base. Split kmers allow rapid comparison and alignment of small genomes, and is particulalry suited for surveillance or outbreak investigation. SKA can produce split kmer files from fasta format assemblies or directly from fastq format read sequences, cluster them, align them with or without a reference sequence and provide various comparison and summary statistics. Currently all testing has been carried out on high-quality Illumina read data, so results for other platforms may vary.
Installation
Installation using Conda
conda install -c bioconda ska
Many thanks to John Lees for creating this Conda recipe!
Installation using Homebrew
brew install brewsci/bio/ska
Many thanks to Torsten Seemann for creating this Brew formula!
Installation from source
SKA can be installed by cloning this repository and running make
Or by Downloading and unpacking the latest release.
Then simply navigate into the SKA directory and run make
The executable will be compiled into a directory named bin. You can either add this bin directory to your path or move the executable into a path directory.
will move the executable to /usr/local/bin.
Requirements
SKA simply requires GNU make and a version of g++ which supports C++11.
Usage
Please read the SKA wiki page for full usage instructions.
License
SKA is free software, licensed under MIT.
Citation
SKA is currently only available as a preprint, so for now, if you use it, please cite: Harris SR. 2018. SKA: Split Kmer Analysis Toolkit for Bacterial Genomic Epidemiology. bioRxiv 453142 doi: https://doi.org/10.1101/453142