Cram-JS

Cram-JS implements decompression and reading of CRAM (Compressed Reference-Aligned Reads) files in JavaScript to enable processing of reference-aligned short-read sequencing data compressed with Huffman coding, subexponential codes, Elias gamma codes, rANS, and gzip in web browsers and Node.js.

Key Features:

• CRAM decompression: Performs on-the-fly decompression and reading of CRAM files.
• Compression algorithm support: Handles data encoded with Huffman coding, subexponential codes, Elias gamma codes, rANS (range Asymmetric Numeral Systems), and gzip.
• Reference-aligned reads: Processes CRAM representation based on alignment of sequencing reads to a reference genome.
• Execution environments: Runs in web browsers and in Node.js server-side environments.
• JavaScript standard: Implemented according to the ES-6 JavaScript standard.
• Genome browser integration: Compatible for integration with web-based genome browsers such as JBrowse and IGV-JS.

Scientific Applications:

• Web-based genome browsing: Enables JBrowse and IGV-JS to directly handle CRAM-compressed genomic data for browser-based analysis.
• Server-side bioinformatics: Enables Node.js-based workflows to process CRAM files without prior decompression.
• Short-read sequencing data processing: Supports analysis and visualization workflows that operate on reference-aligned short-read sequencing data stored in CRAM format.

Methodology:

Implements CRAM file decompression and reading in ES-6 JavaScript, decoding reference-aligned reads compressed via alignment to a reference genome and encoded with Huffman coding, subexponential codes, Elias gamma codes, rANS, and gzip.