HiReNET – Higher-order Repeat Network Exploration Tool

Introduction:

HiReNET is a graph-based pipeline for detecting and analyzing higher-order repeats (HORs) in genomic sequences. The pipeline has been applied to both Arabidopsis thaliana and maize, providing insights into centromeric and knob repeat structure.

Installation:

 
# Clone the Repository
git clone https://github.com/dawelab/HiReNET.git
cd HiReNET

# Build and install
make install

# Add to PATH
echo 'export PATH="$HOME/HiReNET/bin:$PATH"' >> ~/.bashrc
source ~/.bashrc

# Verify
HiReNET --help

Dependencies:

HiReNET relies on common bioinformatics tools. Please make sure these are installed and available in your PATH:

Bioinformatics Tools	R Packages
HMMER (3.4) BLAST+ (2.16.0) BLAT (3.7) SeqKit (2.9.0) BEDTools (2.31.1) bioawk (1.0) MAFFT (7.526) Clustal-Omega (1.2.4) EMBOSS (6.6.0)	dplyr tidyr stringr purrr rlang data.table ggplot2 cowplot igraph caret readr

Input Data:

Input sequences must be provided in FASTA format, with each sequence written on a single line. Chromosome names should use chr1, chr2, chr3, rather than chr01, chr02, chr03. If the provided sequences are not derived directly from a genome assembly, name them sequentially as seq1, seq2, seq3.

	>chr1
	CCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCT
	>chr2
	AGTAATTCTAGAGCTAATACGTGCAACAAACCCCGACTTATGGAAGGGACGCATTTATTA
	...
	>chr10
	CCCTAAACCCTAAACCCTAAACCTAAACCCTAACTAAACCCTAAACCCTAAACCCTAAAC
	>chr11
	GGATCCGTGGTTTCGCGTATCGGCATGGTCGGGAGCTTTTATCTCGGTCTTGTCGTGCGC
	...
	or 
	>seq1
	CCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCTAAACCCT
	>seq2
	AGTAATTCTAGAGCTAATACGTGCAACAAACCCCGACTTATGGAAGGGACGCATTTATTA
	...
	>seq10
	CCCTAAACCCTAAACCCTAAACCTAAACCCTAACTAAACCCTAAACCCTAAACCCTAAAC
	>seq11
	GGATCCGTGGTTTCGCGTATCGGCATGGTCGGGAGCTTTTATCTCGGTCTTGTCGTGCGC
	...

Quick Start:

# Run for a single chromosome or sequence. 
gunzip -k data/test.fasta.gz     # The test.fasta.gz only contains chr1 sequences.
HiReNET runALL \
  --chr chr1 \
  --prefix test \
  --consensus data/AthCEN178_consensus.fasta \
  --seq data/test.fasta \
  --variant data/AthCEN178_consensus_variant.fasta
	
# Run for mutiple chromosomes or sequences. Ey15.fasta is Arabidopsis genome sequences from https://doi.org/10.1038/s41586-023-06062-z.
HiReNET runALL \
  --chr chr1,chr2,chr3,chr4,chr5 \
  --prefix AthCEN178 \
  --consensus data/AthCEN178_consensus.fasta \
  --seq Ey15.fasta \
  --variant data/AthCEN178_consensus_variant.fasta	

Docs

Please see the Wiki for detailed documentation.

Citation