High-throughput sequencing (HTS) data are commonly stored as raw sequencing reads in FASTQ format or as reads mapped to a reference, in SAM format, both with large memory footprints. Worldwide growth of HTS data has prompted the development of compression methods that aim to significantly reduce HTS data size. Here we report on a benchmarking study of available compression methods on a comprehensive set of HTS data using an automated framework.

In this paper, we compare the video codecs AV1 (version 1.0.0-2242 from August 2019), HEVC (HM and x265), AVC (x264), the exploration software JEM which is based on HEVC, and the VVC (successor of HEVC) test model VTM (version 4.0 from February 2019) under two fair and balanced configurations: All Intra for the assessment of intra coding and Maximum Coding Efficiency with all codecs being tuned for their best coding efficiency settings. VTM achieves the highest coding efficiency in both configurations, followed by JEM and AV1. The worst coding efficiency is achieved by x264 and x265, even in the placebo preset for highest coding efficiency. AV1 gained a lot in terms of coding efficiency compared to previous versions and now outperforms HM by 24% BD-Rate gains. VTM gains 5% over AV1 in terms of BD-Rates. By reporting separate numbers for JVET and AOM test sequences, it is ensured that no bias in the test sequences exists. When comparing only intra coding tools, it is observed that the complexity increases exponentially for linearly increasing coding efficiency.

Supplementary data are available at Bioinformatics online.