Tom Paridaens1, Glenn Van Wallendael1, Wesley De Neve1,2,3, Peter Lambert1. 1. Department of Electronics and Information Systems, IDLab, Ghent University - IMEC, Ghent, Belgium. 2. Center for Biotech Data Science, Ghent University Global Campus, Songdo, Incheon 305-701, Republic of Korea. 3. Image and Video Systems Lab, KAIST, Daejeon 305-732, Republic of Korea.
Abstract
Motivation: The past decade has seen the introduction of new technologies that significantly lowered the cost of genome sequencing. As a result, the amount of genomic data that must be stored and transmitted is increasing exponentially. To mitigate storage and transmission issues, we introduce a framework for lossless compression of quality scores. Results: This article proposes AQUa, an adaptive framework for lossless compression of quality scores. To compress these quality scores, AQUa makes use of a configurable set of coding tools, extended with a Context-Adaptive Binary Arithmetic Coding scheme. When benchmarking AQUa against generic single-pass compressors, file sizes are reduced by up to 38.49% when comparing with GNU Gzip and by up to 6.48% when comparing with 7-Zip at the Ultra Setting, while still providing support for random access. When comparing AQUa with the purpose-built, single-pass, and state-of-the-art compressor SCALCE, which does not support random access, file sizes are reduced by up to 21.14%. When comparing AQUa with the purpose-built, dual-pass, and state-of-the-art compressor QVZ, which does not support random access, file sizes are larger by 6.42-33.47%. However, for one test file, the file size is 0.38% smaller, illustrating the strength of our single-pass compression framework. This work has been spurred by the current activity on genomic information representation (MPEG-G) within the ISO/IEC SC29/WG11 technical committee. Availability and implementation: The software is available on Github: https://github.com/tparidae/AQUa. Contact: tom.paridaens@ugent.be.
Motivation: The past decade has seen the introduction of new technologies that significantly lowered the cost of genome sequencing. As a result, the amount of genomic data that must be stored and transmitted is increasing exponentially. To mitigate storage and transmission issues, we introduce a framework for lossless compression of quality scores. Results: This article proposes AQUa, an adaptive framework for lossless compression of quality scores. To compress these quality scores, AQUa makes use of a configurable set of coding tools, extended with a Context-Adaptive Binary Arithmetic Coding scheme. When benchmarking AQUa against generic single-pass compressors, file sizes are reduced by up to 38.49% when comparing with GNU Gzip and by up to 6.48% when comparing with 7-Zip at the Ultra Setting, while still providing support for random access. When comparing AQUa with the purpose-built, single-pass, and state-of-the-art compressor SCALCE, which does not support random access, file sizes are reduced by up to 21.14%. When comparing AQUa with the purpose-built, dual-pass, and state-of-the-art compressor QVZ, which does not support random access, file sizes are larger by 6.42-33.47%. However, for one test file, the file size is 0.38% smaller, illustrating the strength of our single-pass compression framework. This work has been spurred by the current activity on genomic information representation (MPEG-G) within the ISO/IEC SC29/WG11 technical committee. Availability and implementation: The software is available on Github: https://github.com/tparidae/AQUa. Contact: tom.paridaens@ugent.be.