# Execution environment used to produce simulated data for the manuscript

## Title
qc3C - reference-free quality control for Hi-C sequencing data

## Authors
- matthew z. demaere [*1]
- aaron e. darling [1]

## Affiliation
1. ithree institute, University of Technology Sydney
\*. corresponding author

## Description
This repository contains the details, setup information and source code
used in the simulation sweep.

## Steps
1. create the necessary conda environments as described in create_setup.sh
2. activate the qc3c conda environment
3. launch the from_scratch.nf Nextflow workflow.
  a. expected command line parameters are "reference", and "out_dir".

## Example
```
conda activate qc3c
nextflow run from_scratch.nf --reference Ecoli_K12-MG1655.fna --out_dir sim_out
```

