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

Robert Buels; Shihab Dider; Colin Diesh; James Robinson; Ian Holmes

doi:10.1093/bioinformatics/btz384

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

Bioinformatics. 2019 Nov 1;35(21):4451-4452. doi: 10.1093/bioinformatics/btz384.

Authors

Robert Buels¹, Shihab Dider¹, Colin Diesh¹, James Robinson², Ian Holmes¹

Affiliations

¹ Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
² Broad Institute, Cambridge, MA, USA.

Abstract

Motivation: The CRAM format addresses rising DNA storage costs for short-read sequencing by aligning reads to a reference genome and encoding the resulting alignment with Huffman, subexponential, Elias gamma, rANS, gzip and other codes. The CRAM codec is complex, and until now, there has been no JavaScript implementation.

Results: We have developed a JavaScript library, Cram-JS, that natively reads and decompresses the CRAM format on-the-fly. The library is used in the JBrowse and IGV-JS genome browsers and can readily be used by other JavaScript applications, in the web browser or in Node.

Availability and implementation: Cram-JS is written to the ES-6 standard and is available from the GitHub repository at https://github.com/GMOD/cram-js.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

DNA
Genome*
Software*
Web Browser

Substances

DNA

Abstract

Publication types

MeSH terms

Substances

Grants and funding