HELIOS: High-speed sequence alignment in optics
Table 19
Processing time and memory usage to align PacBio and Illumina reads to the Arabidopsis and Human reference genomes by HELIOS optical architecture, compared to BLASR, BWA-MEM, Bowtie2, Nucmer4, Moiré Technique, HAWPOD, and OptCAM.
In this regard, the analytical estimation of the processing times of the HELIOS optical architecture, OptCAM, HAWPOD, and Moiré Technique, are reported by employing a typical graphene-based modulator with an aperture size of 1024 × 1024 pixels and a 100 MHz switching rate. In versus, the processing times of Nucmer4, Bowtie2, BWA-MEM, and BLASR are measured on a dual-CPU, 32-core AMD Opteron 6276 computer with 256 GB of DDR3 PC3–12800 RAM, using 32 parallel threads, as reported in [14]. The report includes the times to build the genome index and to align the sequences. Moreover, the processing times of HELIOS optical architecture are also reported for more recently developed modulators with various aperture sizes, such as 1920 × 1080 and 4096 × 4096 pixels, as well as various switching rates, including 35 GHz [72] and 4.5 THz [67].