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

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

Robert Buels  1 , Shihab Dider  1 , Colin Diesh  1 , James Robinson  2 , Ian Holmes  1
Affiliations

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

Robert Buels et al. Bioinformatics. .

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.

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Figures

Fig. 1.
Fig. 1.
Each graph depicts the runtimes for the corresponding datasets under different interval lengths. Human Low Coverage and Human Exome refer to the NA12878 Low Coverage WGS and Exome alignments, respectively. The error bars depict variability in runtime due to randomly selected intervals having variable depth of coverage
See this image and copyright information in PMC

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