Table 1 Summary of sequencing and assembly approaches tested
From: Semi-automated assembly of high-quality diploid human reference genomes
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 |
