Metadata-Version: 2.4
Name: sar11-genome-atlas-tools
Version: 0.1.8
Summary: SAR11 Genome Atlas Tools (SGAtools)
Author: SAR11 Genome Atlas team
License-Expression: MIT
Project-URL: Homepage, https://github.com/stsnsn/SGAtools
Project-URL: Repository, https://github.com/stsnsn/SGAtools
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: biopython>=1.80
Requires-Dist: pandas>=2.0
Requires-Dist: pyyaml>=6.0
Requires-Dist: rich>=13.7
Dynamic: license-file

# SAR11 Genome Atlas Tools (SGAtools)

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SGAtools is a command-line toolkit for SAR11 Genome Atlas orthologous-group
mapping and phylogenetic classification.

## Install
Version 0.1.8 is the latest release.
```bash
conda create -n sga-tools -c conda-forge -c bioconda sar11-genome-atlas-tools
conda activate sga-tools
```

## Check the installation

```bash
sga-db --version
sga-mapper --version
sga-classify --version
sga-run --version
```

## Quick use

### `sga-mapper`

Map proteins in an amino-acid FASTA file to SAR11 Genome Atlas orthologous
groups and write a per-protein annotation table.

```bash
sga-mapper proteins.faa --output-dir results/mapper
```

### `sga-classify`

Classify a nucleotide genome using marker extraction, phylogenetic placement,
and nearest-genome ANI.

```bash
sga-classify genome.fna --output-dir results/classifier
```

To generate only the concatenated marker alignment from nucleotide or protein
input:

```bash
sga-classify proteins.faa --onlyalign --output-dir results/alignment
```

### `sga-run`

Run gene prediction, orthologous-group mapping, and full classification as one
workflow.

```bash
sga-run genome.fna --output-dir results/run
```

All three commands also accept directories for batch processing. Runtime
databases are downloaded automatically on first use and cached for later runs.

See the [SGAtools Wiki](https://github.com/stsnsn/SGAtools/wiki) for detailed
installation options, command reference, input and output formats, database
management, and troubleshooting.
