Table 2.
Statistics of human genome assemblies generated with various data types and assembly algorithms
| Genome assembly | Data type [coverage; read N50 (kb)] | Assembler | Size (Mb) | # of contigs | Contig N50 (Mb) | Estimated cost | Ref. |
|---|---|---|---|---|---|---|---|
| hg1 | Multi-technology | GigAssembler, PHRAP | 2.69 | 149,821 | 0.082 | $300,000,000 | 72 |
| hg38 | Multi-technology | Multiple algorithms | 3.01 | 998 | 57.88 | not determined | 161 |
| YH | Illumina (56-fold; <0.075) | SOAPdenovo | 2.91 | 361,157 | 0.02 | $1,600a | 162 |
| CHM13 | PacBio CLR (77-fold; 17.5) | FALCON | 2.88 | 1,916 | 29.30 | $2,700b | 30 |
| PacBio HiFi (24-fold; 10.9) | FALCON | 3.00 | 2,116 | 31.92 | $4,100b | 52 | |
| Canu | 3.03 | 5,206 | 25.51 | ||||
| PacBio CLR (77-fold; 17.5) and ONT (50-fold; 70.4) | Canu | 2.94 | 590 | 72.00 | $55,000c | 34 | |
| HG002 | PacBio HiFi (28-fold; 13.5) | FALCON | 2.91 | 2,541 | 28.95 | $2,700b | 53 |
| PacBio HiFi (28-fold; 13.5) | Canu | 3.42 | 18,006 | 22.78 | |||
| ONT (47-fold; 48.7) | Shasta | 2.80 | 1,847 | 23.34 | $5,000d | 36 | |
| Flye | 2.82 | 1,627 | 31.25 | ||||
| Canu | 2.90 | 767 | 33.06 | ||||
| NA12878 | Illumina (103-fold; 0.101) | ALLPATHS-LG | 2.79 | 231,194 | 0.02 | $2,900a | 163 |
| ONT (29-fold; 10.6 5-fold; 99.8) | Flye | 2.82 | 782 | 18.18 | $4,000d | 76 | |
| Canu | 2.82 | 798 | 10.41 | 35 | |||
| NA12878 (phased) | PacBio HiFi (30-fold; 10.0) | Peregrine | 2.97 [H1] 2.97 [H2] | 9,334 [H1] 9,127 [H2] | 19.6 [H1] 18.7 [H2] | $4,100b | 22 |
| HG00733 | ONT (73-fold; 29.6) | Shasta | 2.78 | 2,150 | 24.43 | $6,000d | 36 |
| Flye | 2.81 | 1,852 | 28.76 | ||||
| Canu | 2.90 | 778 | 44.76 | ||||
| HG00733 (phased) | PacBio HiFi (33-fold; 13.4) and Strand-seq (5-fold) | Peregrine | 2.90 [H1] 2.91 [H2] | 2,618 [H1] 2,557 [H2] | 28.0 [H1] 29.2 [H2] | $9,000e | 91 |
Multi-technology: Clone-by-clone hierarchical sequencing with short and Sanger reads.
H1 and H2 refer to the first and second haplotype in the diploid genome assembly, respectively.
a
Current cost when generated on the NovaSeq using S4 flow cells and multiplexing.
b
Current cost when generated on the Sequel II.
c
Current cost when generated on the Sequel II (PacBio CLR) and GridION (ONT).
d
Current cost when generated on the PromethION.
e
Current cost when generated on the Sequel II (PacBio HiFi) and HiSeq 2500 (Illumina).
All estimates are listed in USD and exclude the cost for labor, instrumentation, maintenance, and computer resources.