https://github.com/databio/seqcosts
https://github.com/databio/seqcosts
Last synced: 3 months ago
JSON representation
- Host: GitHub
- URL: https://github.com/databio/seqcosts
- Owner: databio
- Created: 2021-12-07T17:04:29.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2023-08-30T13:45:24.000Z (almost 3 years ago)
- Last Synced: 2025-06-28T02:01:58.952Z (12 months ago)
- Language: HTML
- Homepage: https://databio.org/seqcosts
- Size: 354 KB
- Stars: 0
- Watchers: 1
- Forks: 1
- Open Issues: 0
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Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# SeqCosts
This [GitHub repository](https://github.com/databio/seqcosts) provides an API and visualization of the cost of sequencing over time. Sequencing cost data comes from [NHGRI DNA sequencing costs](https://www.genome.gov/about-genomics/fact-sheets/DNA-Sequencing-Costs-Data). It also contains data for the growth of sequence data in SRA, with data from [SRA stats](https://www.ncbi.nlm.nih.gov/Traces/sra/sra_stat.cgi).
## Motivation
I like to use these plots showing the rapid decrease in sequencing costs in lectures and presentations, or the rapid growth of available sequences, but it was a challenge to keep the plots up-to-date. The plots and data provided directly from NHGRI was not amenable to be permanently linked in a lecture that would auto update, because URLs would change, new plots would be produced rather than updating old links with new data, etc. To make it more useful, I needed a stable URL for data and visualization. So, I made one and put it here so that anyone can update the data. I have simply reformatted the data to make it more FAIR; instead of an excel spreadsheet and an graphical image, I provide an API to access the data, and a vega-lite dynamic plot that just retrieves that data. This, hosted in a persistent spot, makes it possible to produce presentations that are always automatically up-to-date.
## Use
You can get the raw CSV data at:
- Costs: [https://databio.org/seqcosts/data/sequencing_cost.csv](https://databio.org/seqcosts/data/sequencing_cost.csv).
- SRA content: [https://databio.org/seqcosts/data/sra_stat.csv](https://databio.org/seqcosts/data/sra_stat.csv).
## View
You can view corresponding vega-lite visualizations at:
- Costs: [https://databio.org/seqcosts/cost.html](https://databio.org/seqcosts/cost.html).
- SRA data: [https://databio.org/seqcosts/sra.html](https://databio.org/seqcosts/sra.html).
## Embed
If you want to use the plot in a presentation or web page, you have two options
### Use javascript directly
You can look at how I embedded it in the html pages above and just do something similar to use the underlying data however you want.
### Use an iframe.
You can embed the HTML page using an `` like this:
```
## Update
If you use this and notice it's not updated, please add any new rows to `data/sequencing_costs.csv` via Pull Request.