Identification of transposable element families from pangenome polymorphisms

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.

0- Installing

Simply download pantera.R and make it executable chmod +x pantera.R or run with Rscript Rscript pantera.R

1- Prepare your gfa files

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- Obtain the library from the gfa files

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

3- Classify the library obtained

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

3 a- (Optional) Identify structural features in the sequences

pantercheck.R pantera_lib.fa.classified

This will produce a file pantera_lib.fa.classified.benchmark2 with the following fields:

• Column 1: sequence name
• Column 2: sequence length
• Column 3: LTR length
• Column 4: TIR length
• Column 5: polyA length
• Column 6: Sequence repetitiveness (lower means less repetitive)

Data example

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.

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Requirements

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.

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Citing pantera

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