SAR11 Genome Atlas Tools (SGAtools)

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

Install

Version 0.1.9 is the latest release.

conda create -n sga-tools -c conda-forge -c bioconda sar11-genome-atlas-tools
conda activate sga-tools

Check the installation

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.

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

sga-classify

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

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

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

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

sga-run

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

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 for detailed installation options, command reference, input and output formats, database management, and troubleshooting.