Identify target and neighbor genomes for marker discovery.
Genetic markers are genomic regions that are common to a set of target
organisms and absent from all other organisms. This absence is often
tested by running marker candidates against comprehensive sequence
databases like GenBank. Any
hit outside the targets is interpreted as cross-reactivity and
removed. However, for large candidate sets a search of
GenBank can be time
consuming. It is also not necessary, as evolution tells us the vast
majority of cross-reactive material is contained in the targets'
closest phylogenetic neighbors. The programs in neighbors help
identify the target and neighbor genomes listed in the current
assembly reports of
GenBank,
and
RefSeq. If
a genome is listed in both data sources, neighbors picks the RefSeq
accession.
Given a sample of target genomes and a sample of neighbor genomes
discovered with neighbors, the regions common to the targets that
are absent form the neighbors are good marker candidates. The program
fur is one example of a program
for identifying such regions. Once found, the sensitivity and
specificity of the marker candidates can quantified using, for
example, the programs in prim.
Bernhard Haubold, [email protected]
If you are on a Ubuntu system like Ubuntu on wsl under MS-Windows or the Ubuntu Docker container, you can clone the repository and change into it.
git clone https://github.com/evolbioinf/neighbors
cd neighbors
Then install the additional dependencies by running the script
setup.sh.
bash scripts/setup.sh
Make the programs.
make
The directory bin now contains the ten executables of the
package. Put them somewhere in your PATH. Additional scripts are in
scripts.
The
documentation
comes with a tutorial. To work through it, additional programs need to
be installed. Again, on Ubuntu you can run the script
setupTutorial.sh.
bash scripts/setupTutorial.sh
As an alternative to building neighbors from scratch, we also post it as a docker
container. The container
includes all programs needed to work through the tutorial in
neighborsDoc.pdf.
docker pull itsers/neighbors
docker container run --detach-keys="ctrl-@" -h neighbors -it itsers/neighbors
The command
make docker
starts building a local copy of the docker image.