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.
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.
Authors: James T Robinson; Helga Thorvaldsdóttir; Aaron M Wenger; Ahmet Zehir; Jill P Mesirov Journal: Cancer Res Date: 2017-11-01 Impact factor: 12.701
Authors: Robert Buels; Eric Yao; Colin M Diesh; Richard D Hayes; Monica Munoz-Torres; Gregg Helt; David M Goodstein; Christine G Elsik; Suzanna E Lewis; Lincoln Stein; Ian H Holmes Journal: Genome Biol Date: 2016-04-12 Impact factor: 13.583
Authors: Todd W Harris; Valerio Arnaboldi; Scott Cain; Juancarlos Chan; Wen J Chen; Jaehyoung Cho; Paul Davis; Sibyl Gao; Christian A Grove; Ranjana Kishore; Raymond Y N Lee; Hans-Michael Muller; Cecilia Nakamura; Paulo Nuin; Michael Paulini; Daniela Raciti; Faye H Rodgers; Matthew Russell; Gary Schindelman; Kimberly V Auken; Qinghua Wang; Gary Williams; Adam J Wright; Karen Yook; Kevin L Howe; Tim Schedl; Lincoln Stein; Paul W Sternberg Journal: Nucleic Acids Res Date: 2020-01-08 Impact factor: 16.971