TEPEAK

A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations.

Setup

We recommend running everything inside a conda virtual environment using the latest version of conda (23.9.0 at the time of writing). Some packages installed by older versions of conda may not work properly.

OS requirements

We recommend running everything on a Linux machine. If you're on Windows, you can run everything through a Windows Subsystem for Linux (WSL). The instructions to install and set up a WSL on a Windows machine are available at https://learn.microsoft.com/en-us/windows/wsl/install.

Creating INSurVeyor `conda` environment and installing dependecies.

Create the environment with mamba as it's much faster than conda. You can check if you have mamba installed by running

mamba --version

This should output the version of mamba installed. If mamba is not installed, run

conda install -n base -c conda-forge mamba

to install it into the base environment.

Run the following command to create the insurveyor-env environment and install INSurVeyor along with other dependencies inside the environment.

mamba env create -f environment.yaml

After the environment has been created, activate it by running

conda activate insurveyor-env

Other environment requirements

Please view the wiki for instructions on how to install and set up the NCBI SDK, Picard, Smoove, and verifying that you have an appropriate version of Java installed.

Data requirements

TEPEAK requires the following files to run properly:

Zipped genome reference file
Zipped genome gtf file (for gene annotations)
Sra run list file

The Sra run list file needs to be placed in the TEPEAK directory while the zipped files need to be placed inside the data directory. For example,

TEPEAK/
  snakefile
  config.yaml
  SraRunTable.txt
  data/
    ncbi_dataset.zip
    ncbi_dataset_gtf.zip
  ...

where data is the data directory, ncbi_dataset.zip is the zipped reference genome, ncbi_dataset_gtf.zip is the zipped gtf, and SraRunTable.txt is the SRA run list.

Running TEPEAK

After the required files have been placed in the appropriate locations, edit config.yaml to configure it for the species you'd like to analyse.

For example, to analyse ecoli, the config.yaml file would look like

species: ecoli
data_dir: data #name and path of the data directory
output_dir: output #name and path of the output directory
zipped_ref_genome_filepath: data/ncbi_dataset.zip #zipped reference genome file for ecoli
zipped_gtf_filepath: data/ncbi_dataset_gtf.zip  #zipped gtf file for ecoli
sra_run: 
  filepath: SraRunTable.txt #sra run list for ecoli
  number_of_runs: 4 #number of runs to analyse
threads: 10
low: 0 #lower bp range
high: 10000 #upper bp range
gene: y #(y/n) -- includes gene annotations if 'y'

Note: If you want to include gene annotations, you must have a zipped gtf file.

After the config file and the data directory directory structure has been set up, run the TEPEAK pipeline with

snakemake --cores

If your config file is named something other than config.yaml, run the pipeline with

snakemake --configfile <name and path to config file> --cores

This allows you to define multiple config files for different species and run the pipeline for a specific species. Make sure that the new config file follows the exact same format as above.

Make sure to always run the pipeline with the insurveyor-env activated and from the TEPEAK directory. The pipeline produces two histograms, both of which are located in <output_dir>/<species>/. <species>_insertions_plot.svg is the plot with insertions and <species>_smoove_plot.svg is the plot with deletions.

Note: Delete the contents of prefetch_tmp when finished

ryanlayerlab/TEPEAK