Table 1 Comparison of human de novo assembly and haplotype phasing summary statistics
AK1 | HuRef | YH_2.0 | NA12878 | GRCh38 | |
|---|---|---|---|---|---|
Assembly approach | WGS and BAC | WGS | WGS and fosmid | WGS | BAC and fosmid |
Sequencing and physical mapping | PacBio and BioNano | Sanger | Illumina and CG | PacBio and BioNano | Sanger, FISH, OM and fingerprint contigs |
De novo assembly algorithm | FALCON | Celera | SOAPdenovo2 | Celera and FALCON | Multiple methods |
Phasing approach | De novo | Reference-guided | De novo | Reference-guided | NA |
Scaffold/contig N50 (Mb) | 44.85/17.92 | 17.66/0.11 | 20.52/0.02 | 26.83/1.56 | 67.79/56.41 |
Scaffold/contig L50 | 21/50 | 48/7,164 | 39/40,005 | 37/532 | 16/19 |
No. of scaffolds/contigs | 2,832/4,206 | 4,530/71,333 | 125,643/361,157 | 18,903/21,235 | 735/1,385 |
No. of gaps | 264* | 68,109† | 235,514† | 2,332* | 999† |
Total gap length (Mb) | 37.34 | 34.43 | 105.20 | 146.35 | 159.97 |
Total bases/non-N bases in assembly (bp) | 2,904,207,288 /2,866,687,809 | 2,844,000,504 /2,809,571,127 | 2,911,235,363 /2,806,031,133 | 3,176,574,379 /3,030,222,093 | 3,209,286,105 /3,049,316,098 |
Phased block N50 (Mb) | 11.55 | 0.35 | NA | 0.15 | NA |
No. of haplotigs | 18,964 | NA | 24,597 | NA | NA |
Haplotig N50 (kb) | 875 | NA | 484 | NA | NA |
Haplotig sum (bp) | 4,804,460,182 | NA | 5,152,727,603 | NA | NA |
