HiCAT-human

We proposed a modified version of our previous HOR annotation tool HiCAT for automatically annotating centromere HOR patterns from both HiFi reads and assemblies of multiple human samples.

Dependencies

Python 3.9.13

Development environment: Linux

Development tool: Pycharm

Packages	Version
biopython	1.79
joblib	1.1.0
lastz	1.04.22
matplotlib	3.5.1
numpy	1.22.3
pandas	1.4.0
python-edlib	1.3.9
python-levenshtein	0.12.2
scikit-learn	1.0.2
seqtk	1.2
setuptools	61.2.0

StringDecomposer version 1.1.2.

Installation

Source code (g++ version 5.3.1 or higher for stringdecomposer)

#install
conda install -y --file requirements.txt
cd ./stringdecomposer && make

Quick start

Only reads (A combination of reads annotation and aggregation)

python HiCAT_human.py only_reads -r INPUT_READS_DIR -rs READS_SAMPLE_FILE -o READS_OUTPUT_DIR -th THREAD

For more details, please use -h .

• input_reads_dir should contain the fasta format read file of all samples and corresponding .fai file.

  sample1.fasta
  sample1.fasta.fai
  sample2.fasta
  sample2.fasta.fai
  

• reads_sample_file should be a two-column file record all sample names and gender, \t separator.

  sample1	male
  sample2	female
  

• reads_output_diris the output directory.

• th is number of threads.

Reads with assembly (a combination of reads annotation，reads aggregation, assembly annotation and assembly matching to reads)

HiCAT_human.py reads_with_assembly -r INPUT_READS_DIR -rs READS_SAMPLE_FILE -o READS_OUTPUT_DIR -th THREAD -a INPUT_ASSEMBLY_DIR -as ASSEMBLY_SAMPLE_FILE

For more details, please use -h .

• input_reads_dir should contain the fasta format read file of all samples and corresponding .fai file.

• reads_sample_file should be a two-column file record all sample names and gender, \t separator.

• reads_output_diris the output directory.

• th is number of threads.

• input_assembly_dir should contain the fasta format assembly file of all samples and corresponding .fai file.

  assembly1.fasta
  assembly1.fasta.fai
  assembly2.fasta
  assembly2.fasta.fai
  

  The name of chromosomes in assembly file should start with 'chr'.

  >chr1
  ACGTACGTACGTCAGATCTACGCATAGTGTGCTA...
  >chr2
  CACAGTGGTGGTGTGGGTTACTACACA...
  

• assembly_sample_file should be a text file record one sample name per line.

  assembly1
  assembly2
  

Contact

If you have any questions, please feel free to contact: [email protected], [email protected], [email protected]

Reference

Please cite the following paper when you use HiCAT-human in your work

Shenghan Gao, Yimeng Zhang, Stephen James Bush, Bo Wang, Xiaofei Yang, Kai Ye bioRxiv 2024.01.26.577337; doi: https://doi.org/10.1101/2024.01.26.577337