Costs assosiated with DNA sequencing since 2001

core

Files Size Format Created Updated License Source
2 10kB csv zip 1 week ago ODC-PDDL-1.0 Sequencing Cost Table
DNA Sequencing Costs Data Description > For many years, the National Human Genome Research Institute (NHGRI) has tracked the costs associated with DNA sequencing performed at the sequencing centers funded by the Institute. This information has served as an important benchmark for assessing read more
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Data Files

File Description Size Last changed Download Other formats
sequencing-costs [csv] 2kB sequencing-costs [csv] sequencing-costs [json] (4kB)
datapackage_zip [zip] Compressed versions of dataset. Includes normalized CSV and JSON data with original data and datapackage.json. 4kB datapackage_zip [zip]

sequencing-costs  

This is a preview version. There might be more data in the original version.

Field information

Field Name Order Type (Format) Description
Date 1 date (%Y-%m-%d) Date format YYYY-MM
Cost per Mb 2 number The cost of determining one megabase (Mb; a million bases) of DNA sequence of a specified quality
Cost per Genome 3 number The cost of sequencing a human-sized genome

datapackage_zip  

This is a preview version. There might be more data in the original version.

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DNA Sequencing Costs

Data

Description

For many years, the National Human Genome Research Institute (NHGRI) has tracked the costs associated with DNA sequencing performed at the sequencing centers funded by the Institute. This information has served as an important benchmark for assessing improvements in DNA sequencing technologies and for establishing the DNA sequencing capacity of the NHGRI Genome Sequencing Program (GSP). Here, NHGRI provides an analysis of these data, which gives one view of the remarkable improvements in DNA sequencing technologies and data-production pipelines in recent years.

Temporal coverage

2001-2015

Further Information

For further information regarding cost categories, DNA Sequencing Technologies, Quality and Genome Coverage please visit: http://www.genome.gov/sequencingcosts/

Citations

  1. Wetterstrand KA. DNA Sequencing Costs: Data from the NHGRI Genome Sequencing Program (GSP) Available at: www.genome.gov/sequencingcosts. Accessed [21-12-2015].

Sources

Data Preparation

Requirements

Python 2 together with modules urllib and datautil are required in order to process the data.

Processing

Run the following script from this directory to download and process the data:

make

Resources

  • The raw data are stored on directory ./archive/.
  • The processed data are stored on directory ./data.

License

ODC-PDDL-1.0

This Data Package is made available under the Public Domain Dedication and License v1.0 whose full text can be found at: http://www.opendatacommons.org/licenses/pddl/1.0/

Import into your tool

If you are using R here's how to get the data you want quickly loaded:

install.packages("jsonlite")
library("jsonlite")

json_file <- "http://datahub.io/core/genome-sequencing-costs/datapackage.json"
json_data <- fromJSON(paste(readLines(json_file), collapse=""))

# access csv file by the index starting from 1
path_to_file = json_data$resources[[1]]$path
data <- read.csv(url(path_to_file))
print(data)

In order to work with Data Packages in Pandas you need to install the Frictionless Data data package library and the pandas extension:

pip install datapackage
pip install jsontableschema-pandas

To get the data run following code:

import datapackage

data_url = "http://datahub.io/core/genome-sequencing-costs/datapackage.json"

# to load Data Package into storage
storage = datapackage.push_datapackage(data_url, 'pandas')

# data frames available (corresponding to data files in original dataset)
storage.buckets

# you can access datasets inside storage, e.g. the first one:
storage[storage.buckets[0]]

For Python, first install the `datapackage` library (all the datasets on DataHub are Data Packages):

pip install datapackage

To get Data Package into your Python environment, run following code:

from datapackage import Package

package = Package('http://datahub.io/core/genome-sequencing-costs/datapackage.json')

# get list of resources:
resources = package.descriptor['resources']
resourceList = [resources[x]['name'] for x in range(0, len(resources))]
print(resourceList)

data = package.resources[0].read()
print(data)

If you are using JavaScript, please, follow instructions below:

Install data.js module using npm:

  $ npm install data.js

Once the package is installed, use the following code snippet:

const {Dataset} = require('data.js')

const path = 'http://datahub.io/core/genome-sequencing-costs/datapackage.json'

// We're using self-invoking function here as we want to use async-await syntax:
(async () => {
  const dataset = await Dataset.load(path)

  // Get the first data file in this dataset
  const file = dataset.resources[0]
  // Get a raw stream
  const stream = await file.stream()
  // entire file as a buffer (be careful with large files!)
  const buffer = await file.buffer
})()

Install the datapackage library created specially for Ruby language using gem:

gem install datapackage

Now get the dataset and read the data:

require 'datapackage'

path = 'http://datahub.io/core/genome-sequencing-costs/datapackage.json'

package = DataPackage::Package.new(path)
# So package variable contains metadata. You can see it:
puts package

# Read data itself:
resource = package.resources[0]
data = resource.read
puts data
Datapackage.json