A pangenome is a collection of genomes or haplotypes that can be aligned and stored as a variation graph in gfa format. pantera receives as input a list of gfa files of non overlapping variation graphs and produces a library of transposable elements found to be polymorphic on that pangenome.
Simply download pantera.R and make it executable chmod +x pantera.R or run with Rscript Rscript pantera.R
Use pggb to create the pangenome from your starting genome sequences. In its most basic form:
1.1- Create a sigle file for each chromosome combining their fasta files.
cat *.fa yourspecies.chr1.fa
1.2- Compress and index the file.
bgzip -@ 4 yourspecies.chr1.fa
samtools faidx yourspecies.chr1.fa.gz
1.3- Create a pangenome for each chromosome. -n is the number of haplotypes/genomes included. -t is the number of threads.
pggb -i yourspecies.chr1.fa.gz -o output -n 9 -t 16
2.1 Create one file gfas_list with the list of the full paths to the gfa files that will be analyzed.
2.2 Run pantera, with -c as the number of threads.
pantera -g gfas_list -c 16 -o output_folder
pantercheck.R pantera_lib.fa
3.1 Use RepeatClassifier, which is part of the Dfam TE tools, or your classifier of choice to classify the sequences obtained.
RepeatClassifier -consensi pantera_lib.fa
In the folder test there is a gfa example file with the respective outputs that can be used to check if pantera works correctly on your system.
pantera has been tested in Linux with R 4.2.2 to R 4.3.3
pantera requires MAFFT installed and available in the path.
pantercheck requires BLAST installed and available in the path.
If you use pantera in your work, please cite:
Sierra, P., Durbin, R. Identification of transposable element families from pangenome polymorphisms. Mobile DNA 15, 13 (2024). doi.org/10.1186/s13100-024-00323-y