Metadata-Version: 2.4
Name: cutehap
Version: 1.0.3
Summary: Haplotype-resolved genomic structural variation detection with cuteHap
Home-page: https://github.com/Meltpinkg/cuteHap
Author: Shuqi Cao
Author-email: sqcao@stu.hit.edu.cn
License: MIT
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: scipy
Requires-Dist: pysam
Requires-Dist: Biopython
Requires-Dist: Cigar
Requires-Dist: numpy<2.0.0
Requires-Dist: Cython
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# cuteHap

A haplotype-resolved SV detector in phased long read sequencing data.

---
### Installation
We recommand the installation via conda or pip:
```
    $ conda install -c bioconda cutehap
    or
    $ pip install cutehap
```
Alternatively, installing from source with:
```
    $ git clone https://github.com/Meltpinkg/cuteHap.git
    $ cd cuteHap
    $ python setup.py install
```

---	
### Introduction
Structural variations (SVs), as a major category of genomic rearrangements, are capable of altering millions of nucleotides within the human genome. The detection of germline SVs and somatic mosaicism has emerged as a critical frontier in genomic research. Long-read sequencing technologies have demonstrated transformative potential in characterizing these variants. cuteHap is designed to produce high-quality, phased call sets for germline SV detection while simultaneously identifying low-frequency somatic mosaic events. The method delivers high-performance, haplotype-resolved SV detection and comprehensive detection of low-frequency mosaicism. A detailed usage guide documentation is available at [here](https://github.com/Meltpinkg/cuteHap/blob/main/src/benchmarks/documentation.md).

---
### Dependence
    
    1. python3
    2. scipy
    2. pysam
    3. Biopython
    4. cigar
    5. numpy
    6. Cython

---
### Quick Start
```
cuteHap <phased.bam> <reference.fa> <output.vcf> <workdir>
```

---
### Changelog
    cuteHap (v1.0.3)
    1. update the searching algorithm
    
    cuteHap (v1.0.2)
    1. modify the setup instructions
    2. add installation via conda and pypi

    cuteHap (v1.0.1)
    1. update README.md
    2. add user guide documentation
    3. remove unused codes
    
    cuteHap (v1.0.0)
    1. the initial version of cuteHap

---
### Contact
For advising, bug reporting and requiring help, please post on [Github Issue](https://github.com/Meltpinkg/cuteHap/issues) or contact sqcao@stu.hit.edu.cn.
