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Cram-JS: reference-based decompression in node and the browser.

Robert Buels1, Shihab Dider1, Colin Diesh1

  • 1Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.

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|May 18, 2019
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Summary
This summary is machine-generated.

A new JavaScript library, Cram-JS, enables on-the-fly reading and decompression of the CRAM format. This addresses the lack of JavaScript implementations for efficient DNA storage in genomics.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomic Data Compression

Background:

  • Rising DNA storage costs for short-read sequencing necessitate efficient data formats.
  • The CRAM format offers a solution by compressing aligned sequencing reads.
  • A lack of JavaScript implementations hindered CRAM integration in web-based tools.

Purpose of the Study:

  • To develop a native JavaScript library for reading and decompressing CRAM files.
  • To enable seamless integration of CRAM data into web applications and genome browsers.

Main Methods:

  • Development of Cram-JS, a JavaScript library adhering to the ES-6 standard.
  • Implementation of on-the-fly reading and decompression of the CRAM format.
  • Utilizing various compression codes including Huffman, subexponential, Elias gamma, rANS, and gzip.

Main Results:

  • Successful creation of Cram-JS, a functional JavaScript library for CRAM format.
  • Cram-JS enables native, on-the-fly CRAM file processing in web browsers and Node.js.
  • The library is already integrated into JBrowse and IGV-JS genome browsers.

Conclusions:

  • Cram-JS overcomes the previous limitation of no JavaScript CRAM implementation.
  • The library facilitates wider adoption of the CRAM format in web-based bioinformatics.
  • Cram-JS enhances accessibility and usability of genomic data for researchers.