Table 1.
Summary of sequencing and assembly approaches tested
| ID | Pipeline | Technologies | Contigs | Scaffolders | Team |
|---|---|---|---|---|---|
| Diploid contig and scaffold assemblies | |||||
| asm23a,b | Trio VGP | CLR, 10X, BN and Hi-C | Trio Canu | Trio based: Scaff10x, Bionano solve and Salsa | Rockefeller |
| asm10a,b | DipAsm | HiFi and HiC | Peregrine | DipAsm, 3D-DNA, HapCUT2 and Whatshap | UCPH |
| asm2a,b | DipAsm HiRise | HiFi and HiC | Peregrine | HiRise and HapCUT2 | Dovetail |
| asm22a,b | DipAsm Salsa | HiFi and HiC | Peregrine | Salsa and HapCUT2 | Dovetail |
| asm14a,b | PGAS | HiFi and Strand-seq | Peregrine | SaaRclust | HHU + UW |
| asm17a,b | CrossStitch | HiFi, ONT-UL and HiC | CrossStitch | Ref-based to GRCh38 and HapCUT2 | JHU |
| Diploid contig assemblies | |||||
| asm6a,b | Trio Flye ONT std | ONT | Trio Flye | NA | NHGRI |
| asm7a,b | Trio Flye ONT-UL | ONT-UL more than 100 kb | Trio Flye | NA | NHGRI |
| asm19a,b | Trio HiCanu | HiFi | Trio HiCanu | NA | NHGRI |
| asm20a,b | Trio HiPeregrine | HiFi | Trio Peregrine | NA | NHGRI |
| asm9a,b | Trio hifiasm | HiFi | Trio hifiasm | NA | DFCI Harvard |
| asm11a,b | DipAsm HiRise | HiFi and HiC | Peregrine | NA | UCPH |
| asm3a,b | Peregrine HiFi 25 kb | HiFi long | Peregrine | NA | FBDS |
| asm4a,b | Peregrine HiFi 20 kb | HiFi | Peregrine | NA | FBDS |
| asm16a,b | FALCON Unzip | HiFi | FALCON unzip | NA | PacBio |
| asm8a,b | HiCanu | HiFi | HiCanu and Purge_dups | NA | NHGRI |
| Merged haploid contig and scaffold assemblies | |||||
| asm5 | Flye ONT | ONT and HiFi | Flye | Flye | UCSD |
| asm18 | Shasta ONT HiRise | ONT-UL and Hi-C | Shasta | HiRise | UCSC-CZI |
| asm21 | Shasta ONT Salsa | ONT-UL and Hi-C | Shasta | Salsa2 | UCSC-CZI |
| asm15 | MaSuRCA Flye ONT | ONT-UL more than 120 kb and HiFi | Flye | Reference based to GRCh38 and MaSuRCA | JHU |
| asm1 | MaSuRCA Combo | Old ONT, Ill and HiFi | MaSuRCA | Reference based to GRCh38 and MaSuRCA | JHU |
| Merged haploid contig assemblies | |||||
| asm3a | Peregrine HiFi 25K | HiFi long | Peregrine | NA | FBDS |
| asm4a | Peregrine HiFi | HiFi | Peregrine | NA | FBDS |
| asm13 | wtdbg2 HiFi | HiFi and Ill | wtdbg2 | NA | CAAS-AGIS |
| asm12 | NECAT ONT | ONT (no UL) | NECAT | NA | Clemson |
| Final diploid | |||||
| HPRC mat,pat | Trio HPRC v1.0 | HiFi, ONT-UL, BN and Hi-C | Trio hifiasm | Trio based: Bionano Solve, Salsa, gap fill and curated | HPRC |
Listed are the 23 assemblies generated, categorized into four broad types based on whether there were diploid or merged haploid, and scaffolded or contigs only. Details on sequencing technologies are in Supplementary Table 1. Details on assemblers are in Supplementary Table 2a,b. NA, not applicable.