Metadata-Version: 2.4
Name: hgt-site
Version: 0.1.1
Summary: Call candidate horizontal gene transfer sites from host alignments and Kraken2 read classifications
Author: Iraaj Gangavaram
License-Expression: MIT
Project-URL: Homepage, https://github.com/iraajgangavaram/hgt-site
Project-URL: Documentation, https://github.com/iraajgangavaram/hgt-site#readme
Project-URL: Issues, https://github.com/iraajgangavaram/hgt-site/issues
Project-URL: DOI, https://doi.org/10.5281/zenodo.23842712
Keywords: bioinformatics,horizontal gene transfer,genomics,kraken2,metagenomics
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Operating System :: MacOS
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: pysam>=0.21
Provides-Extra: test
Requires-Dist: pytest; extra == "test"
Dynamic: license-file

# hgt-site

hgt-site finds places where DNA from bacteria or other organisms may have been inserted into a host genome, such as a human genome, using sequencing data. Most bacterial reads in these samples come from contamination or from DNA fragments joined by chance in the lab, so hgt-site checks each possible site against what chance alone would produce and keeps only the sites with clearly more support.

It takes paired-end reads aligned to the host (BAM, CRAM or SAM) and Kraken2 classifications of the reads that did not align, and writes a table of candidate sites. It works with any host alignment and Kraken2 output, including the files produced by nf-core/hgtseq.

## Installation

```bash
pip install hgt-site
```

## Usage

```bash
hgt-site call \
  --bam sample.bam \
  --kraken sample.kraken2.txt \
  --host-taxid 9606 \
  --nodes taxonomy/nodes.dmp \
  -o sample.hgt-site.tsv
```

To try it on simulated data with known insertion sites:

```bash
hgt-site simulate -o demo
hgt-site call --bam demo.sam --kraken demo.kraken2.txt --host-taxid 9606 -o demo.tsv
```

## Documentation and benchmarks

The full documentation, the output format and the benchmark results, including a comparison with LGTSeek, are on GitHub: https://github.com/iraajgangavaram/hgt-site

## Citation

If you use hgt-site, please cite it: https://doi.org/10.5281/zenodo.23842712

## Licence

MIT
