Software: STRique
Description
STRique is a python package to analyze repeat expansion and methylation states of short tandem repeats (STR) in Oxford Nanopore Technology (ONT) long read sequencing data.
Available Versions
Unspecified: | 0.4.2 |
---|
Docker hub: https://hub.docker.com/r/giesselmann/strique
Home page: https://github.com/giesselmann/STRique
Commands
- STRique.py
- STRique_test.py
- fast5Masker.py
Module
You can load the modules by:
module load biocontainers
module load strique
Example job
Using
#!/bin/sh -l
as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bash
instead.
To run strique on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=strique
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers strique
STRique_test.py
STRique.py index data/ > data/reads.fofn
cat data/c9orf72.sam | STRique.py count ./data/reads.fofn ./models/r9_4_450bps.model ./configs/repeat_config.tsv --config ./configs/STRique.json