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https://github.com/corneliusroemer/desh-data
Sequence lineage information extracted from RKI sequence data repo
https://github.com/corneliusroemer/desh-data
dataset germany lineages pangolin robert-koch-institut sars-cov-2 sequencing
Last synced: 24 days ago
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Sequence lineage information extracted from RKI sequence data repo
- Host: GitHub
- URL: https://github.com/corneliusroemer/desh-data
- Owner: corneliusroemer
- License: unlicense
- Created: 2021-12-25T15:12:40.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2022-05-17T05:30:43.000Z (over 2 years ago)
- Last Synced: 2024-05-11T05:53:32.349Z (6 months ago)
- Topics: dataset, germany, lineages, pangolin, robert-koch-institut, sars-cov-2, sequencing
- Language: Jupyter Notebook
- Homepage:
- Size: 506 MB
- Stars: 24
- Watchers: 3
- Forks: 3
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Pango lineage information for German SARS-CoV-2 sequences
This repository contains a join of the metadata and pango lineage tables of all German SARS-CoV-2 sequences published by the Robert-Koch-Institut on [Github](https://github.com/robert-koch-institut/SARS-CoV-2-Sequenzdaten_aus_Deutschland).
The data here is updated every hour, automatically through a Github action, so whenever new data appears in the RKI repo, you will see it here within at most an hour.
The resulting dataset can be downloaded here, beware it's currently around 50MB in size:
## Omicron share plot
Type `N` means representative surveillance. Type `X` means unknown, but since this is unlikely to be heavily targeted and includes quite a number of labs I include it now in the main plot (hence type `NX`).
## Description of data
Column description:
- IMS_ID: Unique identifier of the sequence
- DATE_DRAW: Date the sample was taken from the patient
- SEQ_REASON: Reason for sequencing, one of:
- X: Unknown
- N: Random sampling
- Y: Targeted sequencing (exact reason unknown)
- A[\]: Targeted sequencing because variant PCR indicated VOC
- PROCESSING_DATE: Date the sample was processed by the RKI and added to Github repo
- SENDING_LAB_PC: Postcode (PLZ) of lab that did the initial PCR
- SEQUENCING_LAB_PC: Postcode (PLZ) of lab that did the sequencing
- lineage: Pango lineage as reported by `pangolin`
- scorpio_call: Alternative, rough, variant as determined by `scorpio` (part of `pangolin`), this is less precise but a bit more robust than `pangolin`.
## Excerpt
Here are the first 10 lines of the dataset.
```csv
IMS_ID,DATE_DRAW,SEQ_REASON,PROCESSING_DATE,SENDING_LAB_PC,SEQUENCING_LAB_PC,lineage,scorpio_call
IMS-10294-CVDP-00001,2021-01-14,X,2021-01-25,40225,40225,B.1.1.297,
IMS-10025-CVDP-00001,2021-01-17,N,2021-01-26,10409,10409,B.1.389,
IMS-10025-CVDP-00002,2021-01-17,N,2021-01-26,10409,10409,B.1.258,
IMS-10025-CVDP-00003,2021-01-17,N,2021-01-26,10409,10409,B.1.177.86,
IMS-10025-CVDP-00004,2021-01-17,N,2021-01-26,10409,10409,B.1.389,
IMS-10025-CVDP-00005,2021-01-18,N,2021-01-26,10409,10409,B.1.160,
IMS-10025-CVDP-00006,2021-01-17,N,2021-01-26,10409,10409,B.1.1.297,
IMS-10025-CVDP-00007,2021-01-18,N,2021-01-26,10409,10409,B.1.177.81,
IMS-10025-CVDP-00008,2021-01-18,N,2021-01-26,10409,10409,B.1.177,
IMS-10025-CVDP-00009,2021-01-18,N,2021-01-26,10409,10409,B.1.1.7,Alpha (B.1.1.7-like)
IMS-10025-CVDP-00010,2021-01-17,N,2021-01-26,10409,10409,B.1.1.7,Alpha (B.1.1.7-like)
IMS-10025-CVDP-00011,2021-01-17,N,2021-01-26,10409,10409,B.1.389,
```
## Suggested import into pandas
You can import the data into pandas as follows:
```python
#%%
import pandas as pd
#%%
df = pd.read_csv(
'https://raw.githubusercontent.com/corneliusroemer/desh-data/main/data/meta_lineages.csv',
index_col=0,
parse_dates=[1,3],
infer_datetime_format=True,
cache_dates=True,
dtype = {'SEQ_REASON': 'category',
'SENDING_LAB_PC': 'category',
'SEQUENCING_LAB_PC': 'category',
'lineage': 'category',
'scorpio_call': 'category'
}
)
#%%
df.rename(columns={
'DATE_DRAW': 'date',
'PROCESSING_DATE': 'processing_date',
'SEQ_REASON': 'reason',
'SENDING_LAB_PC': 'sending_pc',
'SEQUENCING_LAB_PC': 'sequencing_pc',
'lineage': 'lineage',
'scorpio_call': 'scorpio'
},
inplace=True
)
df
```
## License
The underlying files that I use as input are licensed by RKI under CC-BY 4.0, see more details here: .
The software here is licensed under the "Unlicense". You can do with it whatever you want.
For the data, just cite the original source, no need to cite this repo since it's just a trivial join.