https://github.com/gear-genomics/halo
Halo: Haplotype processor
https://github.com/gear-genomics/halo
alignment bam haplotypes single-cell
Last synced: 5 months ago
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Halo: Haplotype processor
- Host: GitHub
- URL: https://github.com/gear-genomics/halo
- Owner: gear-genomics
- License: gpl-3.0
- Created: 2018-07-27T06:26:17.000Z (almost 8 years ago)
- Default Branch: main
- Last Pushed: 2025-12-27T18:56:52.000Z (6 months ago)
- Last Synced: 2025-12-29T15:35:22.527Z (6 months ago)
- Topics: alignment, bam, haplotypes, single-cell
- Language: C++
- Homepage: https://www.gear-genomics.com/halo/
- Size: 5.78 MB
- Stars: 3
- Watchers: 4
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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# Halo: Haplotype processor
[GEAR](https://www.gear-genomics.com/) hosts the `halo` web application at [https://www.gear-genomics.com/halo/](https://www.gear-genomics.com/halo/). The `halo` command-line tool is needed to compute the input file for the `halo` web application.
## Installing halo
The `halo` command-line tool is available as a pre-compiled statically linked binary from [Halo's github release page](https://github.com/gear-genomics/halo/releases/), as a singularity container [SIF file](https://github.com/gear-genomics/halo/releases/) or as a minimal [Docker container](https://hub.docker.com/r/geargenomics/halo/).
```bash
git clone --recursive https://github.com/gear-genomics/halo.git
cd halo/
make all
make install
```
## Usage
Halo is used to create the input JSON file for the [web application](https://www.gear-genomics.com/halo/).
```bash
./bin/halo -h
```
This command-line application was designed for [Strand-Seq](https://en.wikipedia.org/wiki/Single-cell_DNA_template_strand_sequencing) single-cell DNA data but the viewer can also be used for any haplotype-resolved data. To convert the Strand-Seq alignment data into JSON format please provide one input BAM file for each input cell, e.g.:
```bash
halo count -g hg38.fa -o sc.json.gz sc1.bam sc2.bam sc3.bam
```
The output file `sc.json.gz` can then be uploaded and visualized at [https://www.gear-genomics.com/halo/](https://www.gear-genomics.com/halo/).
License
-------
Halo is distributed under the GPLv3 license. Consult the accompanying [LICENSE](https://github.com/gear-genomics/halo/blob/main/LICENSE) file for more details.
Credits
-------
[HTSlib](https://github.com/samtools/htslib) is heavily used for all genomic alignment variant processing. [Boost](https://www.boost.org/) for various data structures and algorithms.