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sr2silo processes short-read nucleotide alignments from .bam files, translates and aligns reads in amino acids, and outputs JSON compatible with LAPIS-SILO v0.8.0+.

sr2silo can also submit these files to Loculus, as attachments to a sequence entry.

Installation

conda install -c bioconda sr2silo

Quick Start

Processing BAM data:

sr2silo process-from-vpipe \
    --input-file input.bam \
    --sample-id SAMPLE_001 \
    --timeline-file timeline.tsv \
    --organism covid \
    --output-fp output.ndjson.zst

Submitting to Loculus:

sr2silo submit-to-loculus \
    --processed-file output.ndjson.zst

Documentation

Full documentation is available at the sr2silo documentation site:

• Configuration - Environment variables and CLI options
• Multi-Organism Support - Supported organisms and adding new ones
• Deployment - Multi-virus cluster deployment
• API Reference - Python API documentation

Development

make setup-dev
conda activate sr2silo-dev
poetry install --with dev
pytest

License

See LICENSE for details.