Table of Contents
- Quick Start
- Hands-on toy example
Pandora is a tool for bacterial genome analysis using a pangenome reference graph (PanRG). It allows gene presence/absence detection and genotyping of SNPs, indels and longer variants in one or a number of samples. Pandora works with Illumina or Nanopore data. For more details, see our paper.
The PanRG is a collection of 'floating' local graphs (PRGs), each representing some orthologous region of interest (e.g. genes, mobile elements or intergenic regions). See https://github.com/leoisl/make_prg for a tool which can construct these PanRGs from a set of aligned sequence files.
Pandora can do the following for a single sample (read dataset):
- Output inferred mosaic of reference sequences for loci (eg genes) from the PRGs which are present in the PanRG;
- Output a VCF showing the variation found within these loci, with respect to any reference path in the PRGs;
- Discovery of new variation not in the PanRG.
For a collection of samples, it can:
- Output a matrix showing inferred presence-absence of each locus in each sample genome;
- Output a multisample pangenome VCF including genotype calls for each sample in each of the loci. Variation is shown with respect to the most informative recombinant path in the PRGs (see our paper).
pandorais not yet a production-ready tool.
Index PanRG file:
pandora index -t 8 <panrg.fa>
Compare first 30X of each Illumina sample to get pangenome matrix and VCF
pandora compare --genotype --illumina --max-covg 30 <panrg.fa> <read_index.tab>
Map Nanopore reads from a single sample to get approximate sequence for genes present
pandora map <panrg.fa> <reads.fq>
Hands-on toy example
You can test
pandora on a toy example following this link.
There is no need to have
No installation needed - precompiled portable binary
You can use
pandora with no installation at all by simply downloading the precompiled binary, and running it.
In this binary, all libraries are linked statically.
chmod +x pandora-linux-precompiled-v0.9.1 ./pandora-linux-precompiled-v0.9.1 -h
- We provide precompiled binaries for Linux OS only;
conda install -c bioconda pandora
You can also download a containerized image of Pandora. Pandora is hosted on Quay and images can be downloaded with the command:
URI="quay.io/rmcolq/pandora" docker pull "$URI" docker run -it "$URI" pandora --help
Alternatively, using singularity:
URI="docker://quay.io/rmcolq/pandora" singularity exec "$URI" pandora --help
Installation from source
This is the hardest way to install
pandora, but that yields the most optimised binary.
A Unix or Mac OS, with a C++11 compiler toolset (e.g.
Download and install
pandoraas follows (this example is using
4to how many threads you want):
git clone --single-branch https://github.com/rmcolq/pandora.git --recursive cd pandora mkdir -p build cd build cmake -DHUNTER_JOBS_NUMBER=4 -DCMAKE_BUILD_TYPE=Release .. make -j4 ctest -VV
- If you want to produce meaningful stack traces in case
binutils-devmust be installed and the
cmakemust receive this additional parameter: