Table 2.

Summary of the main differences between the three types of prominent sequencing technologies. We choose the most capable instrument as a representative of each sequencing technology.

	Short Reads	Ultra-long Reads	Accurate Long Reads
Type of raw sequencing data (before basecalling)	Multiple images of fluorescence intensities for each sequencing cycle	Electrical signal for each DNA segment	Fluorescence traces captured continuously into a 30-hour movie
Input file format for basecalling	BCL or CBCL	FAST5	BAM
Expected size of basecalling input file	One CBCL file of size 350 MB per cycle, lane, and surface	10x the size of the corresponding FASTQ file	Subreads.BAM of size 0.5–1.5 TB
Basecalling algorithm	BCL2FASTQ	Guppy/Bonito (deep neural networks)	CCS
Basecalling time	48 minutes1	142 minutes2	24 hours3
Number of basecalled bases	83.5 Gb1	20 Gb2	200 Gb of HiFi yield3

¹BCL2FASTQ based on SRR2890933, 1.67 billion reads (full 8 lanes) at 50 bp read length [113].

²Using a single V100 GPU, adapted from [111].

³Using CCS v6.0 for a 25 KBases library on 2x64 cores at 2.4 GHz, adapted from [114].