[](http://bioconda.github.io/recipes/gubbins/README.html)
Since the introduction of high-throughput, second-generation DNA sequencing technologies, there has been an enormous increase in the size of datasets being used for estimating bacterial population phylodynamics. Although many phylogenetic techniques are scalable to hundreds of bacterial genomes, methods which have been used for mitigating the effect of mechanisms of horizontal sequence transfer on phylogenetic reconstructions cannot cope with these new datasets. Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences.
Since the introduction of high-throughput, second-generation DNA sequencing technologies, there has been an enormous
increase in the size of datasets being used for estimating bacterial population phylodynamics.
Although many phylogenetic techniques are scalable to hundreds of bacterial genomes, methods which have been used
for mitigating the effect of mechanisms of horizontal sequence transfer on phylogenetic reconstructions cannot cope
with these new datasets. Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm
that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing
a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm
generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run
in only a few hours on alignments of hundreds of bacterial genome sequences.
## Installation
Before you do anything, please have a look at the [Gubbins webpage](http://sanger-pathogens.github.io/gubbins/).
@@ -44,7 +51,7 @@ Before you do anything, please have a look at the [Gubbins webpage](http://sange
There are a number of ways to install Gubbins and details are provided below. If you encounter an issue when installing Gubbins please contact your local system administrator.
@@ -72,16 +79,15 @@ We have a docker container which gets automatically built from the latest versio
The flag `-v` synchronizes a directory on the host machine (here denoted as `<local_dir>`) with a directory in the Docker container (here denoted as `<remote_dir>`).
`<remote_dir>` does not need to exist in the container before the run, a common choice is `/data`.
Note that both `<local_dir>` and `<remote_dir>` must be absolute paths.
The input alignment file must be present in `<local_dir>` (or in one of its subdirectories).
In order to retrieve the files produced by Gubbins, run the program with option `-p`;
the argument of this option must consist of `<remote_dir>`, followed by an arbitrary identifier (here denoted as `<prefix>`).
In order to retrieve the files produced by Gubbins, run the program with option `-p`; the argument of this option must consist of `<remote_dir>`,
followed by an arbitrary identifier (here denoted as `<prefix>`).
### OSX/Linux - from source
This is the most difficult method and is only suitable for someone with advanced computing skills. Please consider using Conda instead.
@@ -136,16 +142,19 @@ Processing options:
--tree_builder, -t
The algorithm to use in the construction of phylogenies in the analysis; can be ‘raxml’, to use RAxML, ‘fasttree’, to use Fasttree, or ‘hybrid’, to use Fasttree for the first iteration and RAxML in all subsequent iterations. Default is raxml
The algorithm to use in the construction of phylogenies in the analysis; can be ‘raxml’, to use RAxML, ‘fasttree’,
to use Fasttree, or ‘hybrid’, to use Fasttree for the first iteration and RAxML in all subsequent iterations. Default is raxml
--iterations, -i
The maximum number of iterations to perform; the algorithm will stop earlier than this if it converges on the same tree in two successive iterations. Default is 5.
--min_snps, -m
The minimum number of base substitutions required to identify a recombination. Default is 3.
--converge_method, -z
Criteria to use to know when to halt iterations [weighted_robinson_foulds|robinson_foulds|recombination]. Default is weighted_robinson_foulds.
Output options:
@@ -164,7 +173,8 @@ Print debugging messages. Default is off.
--no_cleanup, -n
Do not remove files from intermediate iterations. This option will also keep other files created by RAxML and fasttree, which would otherwise be deleted. Default is to only keep files from the final iteration.
Do not remove files from intermediate iterations. This option will also keep other files created by RAxML and fasttree,
which would otherwise be deleted. Default is to only keep files from the final iteration.
--raxml_model, -r
@@ -241,8 +251,10 @@ For more information on this software see the [Gubbins webpage](http://sanger-pa
From version 1.3.5 (25/6/15) to version 1.4.6 (29/2/16) trees were not midpoint rerooted by default. This doesnt have any effect on the recombination detection, but the output trees may not look as expected. Users are advised to upgrade to the latest version.
From version 1.3.5 (25/6/15) to version 1.4.6 (29/2/16) trees were not midpoint rerooted by default.
This doesnt have any effect on the recombination detection, but the output trees may not look as expected. Users are advised to upgrade to the latest version.
### Ancestral sequence reconstruction
From version 2.0.0 onwards, RAxML is used to reconstruction ancestral sequences instead of fastML. RAxML doesnt always produce results as you would expect so the results can be lower quaility than fastML. If you would like to stick with fastML for ancestral sequence reconstruction, please checkout and install v1.4.9.
From version 2.0.0 onwards, RAxML is used to reconstruction ancestral sequences instead of fastML.
RAxML doesnt always produce results as you would expect so the results can be lower quaility than fastML.
If you would like to stick with fastML for ancestral sequence reconstruction, please checkout and install v1.4.9.
