Introduction
When developing a new assembler, we often need to run other assemblers and to compare the results. However, it is not always easy to run others' tools and assembling a large genome may take days or even weeks. To save developers' time, here we provide stable links to multiple public long-read assemblies and their input data if possible. "Stable links" refer to links provided by NCBI, Zenodo, FigShare, etc, which can't be modified by data owners. FTP links or links to S3/GCP buckets are not stable.
Assemblies
In the following tables, the "Source" column indicates the authors who ran the assembler and produced the assembly. Sometimes they may not be the original developer of the assembler. If you use an assembly in the table, please cite the assembler in use and the source publication.
CHM13: homozygous human
| Data | Assembler | Version | Source | Link |
|---|---|---|---|---|
| HiFi | Flye | 2.8 | Dev website | Zenodo |
| HiFi | Falcon | 1.8.1 | Cheng et al | Zenodo |
| HiFi | HiCanu | 2.1 | Cheng et al | Zenodo |
| HiFi | hifiasm | 0.12 | Cheng et al | Zenodo |
| HiFi | Peregrine | 0.1.6.1 | Cheng et al | Zenodo |
| HiFi | pg_asm | 0.3.5 | Dev website | Zenodo |
| ONT | Canu+Helen | 1.8+0.1 | Shafin et al | Zenodo |
| ONT | Flye+Helen | 2.4.2+0.1 | Shafin et al | Zenodo |
| ONT | Flye | 2.8 | Dev website | Zenodo |
| ONT | Shasta+Helen | 0.1.0 | Shafin et al | Zenodo |
| ONT+SR | WenganD | 0.2 | Di Genova et al | Zenodo |
| CLR | Falcon | NCBI |
HG00733: heterozygous human
| Data | Assembler | Version | Type | Source | Link |
|---|---|---|---|---|---|
| HiFi | Falcon | 1.8.1 | Primary | Cheng et al | Zenodo |
| HiFi | HiCanu | 2.1 | Primary | Cheng et al | Zenodo |
| HiFi+SRpat+SRmat | HiCanu | 2.1 | Phased | Cheng et al | hap1, hap2 |
| HiFi | hifiasm | 0.12 | Primary | Cheng et al | Zenodo |
| HiFi+SRpat+SRmat | hifiasm | 0.12 | Phased | Cheng et al | hap1, hap2 |
| HiFi | Peregrine | 0.1.6.1 | Primary | Cheng et al | Zenodo |
| HiFi+SRpat+SRmat | Peregrine | 0.1.6.1 | Phased | Cheng et al | hap1, hap2 |
| HiFi+HiC | DipAsm+Peregrine | Phased | Garg et al | hap1, hap2 | |
| HiFi+StrandSeq | PGAS+Peregrine | Phased | Porubsky et al | hap1, hap2 | |
| ONT | Canu+Helen | 1.8+0.1 | Collapsed | Shafin et al | Zenodo |
| ONT | Flye+Helen | 2.4.2+0.1 | Collapsed | Shafin et al | Zenodo |
| ONT | Shasta+Helen | 0.1.0+0.1 | Collapsed | Shafin et al | Zenodo |
| CLR | Falcon-Unzip | Primary | Kronenberg et al | NCBI | |
| CLR+HiC | Falcon-Phase | Phased | Kronenberg et al | hap1, hap2 | |
| CLR | WenganD | 0.2 | Collapsed | Di Genova et al | Zenodo |