Metadata-Version: 2.1
Name: sam2lca
Version: 0.3.3
Summary: Last Commont Ancestor on SAM/BAM/CRAM alignment files
Home-page: https://github.com/maxibor/sam2lca
License: GNU-GPLv3
Platform: UNKNOWN
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Requires-Dist: click
Requires-Dist: pysam
Requires-Dist: tqdm
Requires-Dist: xopen
Requires-Dist: python-rocksdb
Requires-Dist: ete3
Requires-Dist: pandas
Requires-Dist: ordered-set

![sam2lca-CI](https://github.com/maxibor/sam2lca/workflows/sam2lca-CI/badge.svg) [![Documentation Status](https://readthedocs.org/projects/sam2lca/badge/?version=latest)](https://sam2lca.readthedocs.io/en/latest/?badge=latest)
# sam2lca

[Lowest Common Ancestor](https://en.wikipedia.org/wiki/Lowest_common_ancestor) from a SAM/BAM/CRAM sequence alignment file

## Quick start

Quick analyis of sequencing reads aligned to a DNA database

```bash
sam2lca analyze myfile.bam
```

See all options

```bash
sam2lca --help
sam2lca update-db --help
sam2lca analyze --help
```

## Installation

### From source

```bash
git clone git@github.com:maxibor/sam2lca.git
conda env create -f environment.yml
conda activate sam2lca
pip install git+ssh://git@github.com/maxibor/sam2lca.git
```

### From Conda

```bash
conda install -c conda-forge -c bioconda -c maxibor sam2lca
```
### From Pypi

```bash
pip install sam2lca
```

## Documentation

The documentation is available here: [sam2lca.readthedocs.io](https://sam2lca.readthedocs.io)

