This repository contains the pipeline for assessing telomere length from "Chromosome specific telomere lengths and the minimal functional telomere revealed by nanopore sequencing"
- Minimap2 (https://github.com/lh3/minimap2)
- TideHunter (https://github.com/Xinglab/TideHunter)
- Porechop (https://github.com/rrwick/Porechop)
- samtools (http://www.htslib.org/download/)
- bedtools (https://bedtools.readthedocs.io/en/latest/content/installation.html)
- snakemake (https://snakemake.readthedocs.io/en/stable/getting_started/installation.html)
git clone git@github.com:timplab/Telomere_Length.git
cd Telomere_Length
vim config.yaml
Edit paths in congfig.yaml to the location of software installs and input files
snakemake --snakefile run_telo.snk --cores 8
Additionally, all scripts can run as stand alone executeables (filter.sh and telo_length.R) that take user input from TideHunter and minimap2. Run with -h for instructions.