https://github.com/genspectrum/ingest

https://github.com/genspectrum/ingest

Last synced: 5 days ago
JSON representation

• Host: GitHub
• URL: https://github.com/genspectrum/ingest
• Owner: GenSpectrum
• Created: 2023-10-01T18:18:39.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2025-04-01T12:35:26.000Z (about 2 months ago)
• Last Synced: 2025-04-01T13:34:38.299Z (about 2 months ago)
• Language: Kotlin
• Size: 237 KB
• Stars: 1
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

README

        
# GenSpectrum ingest

## Run with Docker

See help page:

```bash

docker run --rm ghcr.io/genspectrum/ingest:main -h

```

Preprocess GISAID data:

```bash

docker run --rm \

  -v :/data \

  ghcr.io/genspectrum/ingest:main \

  ingest-sc2-gisaid \

  /data \

   \

   \

   \

   \

  /app/gisaid_geoLocationRules.tsv

```

## Internal data format

The program uses `ndjson.zst` as the default format. One JSON entry could look as follows:

```json

{

    "id": "MW12345",

    "metadata": {

        "genbankAccession": "MW12345",

        "sequencingDate": "2022-08-15",

        "country": "Schweiz",

        "pangoLineage": "XBB.1.5"

    },

    "unalignedNucleotideSequences": {

        "main": "AATTCC..."

    },

    "alignedNucleotideSequences": {

        "main": "NNNNNAATTCC..."

    },

    "nucleotideInsertions": {

        // ???

    },

    "alignedAminoAcidSequences": {

        "S": "XXMSR...",

        "ORF1a": "...",

        // ...

    },

    "aminoAcidInsertions": {

        // ???

    }

}

```