Telebuilder

A toolkit for building TE annotations

Installing

Create new mamba/conda environment (recommended)

mamba env create -n telebuilder https://github.com/mlbendall/telebuilder/raw/main/environment.yml

Install using pip

pip install git+https://github.com/mlbendall/telebuilder.git@main#egg=telebuilder

Tools

buildERV

buildERV assembles ERV proviral loci - ERV insertions with recognizable internal regions - by combining genomic regions matching ERV internal regions with flanking LTR sequences. The initial genomic regions, or "hits", along with the associated alignment information are retrieved from the UCSC Genome Browser database (rmsk table). The main arguments include the internal model name and the LTR model names.

Example: HERVH

HERVH elements have internal regions matching the "HERVH-int" model and flanking LTRs matching either "LTR7", "LTR7A", "LTR7B", "LTR7C", or "LTR7Y". An example command to build HERVH would be:

buildERV\
  --genome_build hg38\
  --chrom_sizes chrom.sizes\
  --cytoband cytoband.gtf\
  HERVH HERVH-int LTR7,LTR7A,LTR7B,LTR7C,LTR7Y

where "hg38" is the genome build, "chrom.sizes" is a file with the chromosome names and sizes, and "cytoband.gtf" is a GTF file with cytogenetic band regions.