Published December 13, 2025
| Version 1.0
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Benchmarking alignment strategies for Hi-C reads in metagenomic Hi-C data
Description
This repository contains the source code for the manuscript "Benchmarking alignment strategies for Hi-C reads in metagenomic Hi-C data."
File Descriptions:
- sim3c.yml: Conda environment configuration file for setting up the necessary software dependencies.
- preprocessing.sh: Script for preprocessing raw sequencing data.
- assembly.sh: Script for generating the metagenomic assembly.
- alignment.sh: Script for aligning Hi-C reads to the metagenomic assembly.
- downstream_pair.sh: Script for Hi-C matrix normalization (paired-end reads).
- downstream_single.sh: Script for Hi-C matrix normalization (single-end reads).
- imputecc.sh: Script for metagenomic binning.
Files
README.md
Files
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