Rasmus Kirkegaard 15 September, 2025
Overview of our data for microbial genomic benchmarking. We have sequenced a bunch of mono cultures, and metagenomic samples. Data has been deposited to the ENA (PRJEB85558).
Monocultures:
- Anabaena variabilis PCC 7120 DSM 107007
- Desulfobacca acetoxidans ASRB2 DSM 11109
- Sagittula stellata E-37 DSM 11524
- Salmonella bongori 1224.72 DSM 13772
- Burkholderia cenocepacia J2315 DSM 16553
- Sphaerobacter thermophilus S 6022 DSM 20745
- Zymomonas mobilis subsp. pomaceae Barker I DSM 22645
- Methanocaldococcus jannaschii JAL-1 DSM 2661
- Sphaerotilus natans 6 DSM 6575
- Thermanaerovibrio acidaminovorans Su883 DSM 6589
Mock Metagenomes:
“Real” metagenomes:
- ZymoFecal
- wwtp_NL-09
- wwtp_IL-01
- wwtp_US2-26
- wwtp_IN-06
- wwtp_US1-124
- sediment_MFD04716
- sediment_MFD00905
- sediment_MFD05674
- sediment_MFD10007
- sediment_MFD09779
- soil_MFD00392
- soil_MFD06742
- soil_MFD06229
- soil_MFD02242
- soil_MFD02360
You find a description of this sample here: https://www.dsmz.de/collection/catalogue/details/culture/DSM-107007
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| Anabaena variabilis PCC 7120 DSM 107007 | 1.0.0 | 5.2.0 | fast | hac | NA | sup | NA | mods | pod5 |
| Anabaena variabilis PCC 7120 DSM 107007 | 0.8.2 | 5.0.0 | fast | hac | NA | sup | NA | mods | pod5 |
You find a description of this sample here: https://www.dsmz.de/collection/catalogue/details/culture/DSM-11109
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| Desulfobacca acetoxidans ASRB2 DSM 11109 | 1.0.0 | 5.2.0 | fast | hac | NA | sup | NA | mods | pod5 |
| Desulfobacca acetoxidans ASRB2 DSM 11109 | 0.8.2 | 5.0.0 | fast | hac | NA | sup | NA | mods | pod5 |
You find a description of this sample here: https://www.dsmz.de/collection/catalogue/details/culture/DSM-11524
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| Sagittula stellata E-37 DSM 11524 | 1.0.0 | 5.2.0 | fast | hac | NA | sup | NA | mods | pod5 |
| Sagittula stellata E-37 DSM 11524 | 0.8.2 | 5.0.0 | fast | hac | NA | sup | NA | mods | pod5 |
You find a description of this sample here: https://www.dsmz.de/collection/catalogue/details/culture/DSM-13772
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| Salmonella bongori 1224.72 DSM 13772 | 1.0.0 | 5.2.0 | fast | hac | NA | sup | NA | mods | pod5 |
| Salmonella bongori 1224.72 DSM 13772 | 0.8.2 | 5.0.0 | fast | hac | NA | sup | NA | mods | pod5 |
You find a description of this sample here: https://www.dsmz.de/collection/catalogue/details/culture/DSM-16553
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| Burkholderia cenocepacia J2315 DSM 16553 | 1.0.0 | 5.2.0 | fast | hac | NA | sup | NA | mods | pod5 |
| Burkholderia cenocepacia J2315 DSM 16553 | 0.8.2 | 5.0.0 | fast | hac | NA | sup | NA | mods | pod5 |
You find a description of this sample here: https://www.dsmz.de/collection/catalogue/details/culture/DSM-20745
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| Sphaerobacter thermophilus S 6022 DSM 20745 | 1.0.0 | 5.2.0 | fast | hac | NA | sup | NA | mods | pod5 |
| Sphaerobacter thermophilus S 6022 DSM 20745 | 0.8.2 | 5.0.0 | fast | hac | NA | sup | NA | mods | pod5 |
You find a description of this sample here: https://www.dsmz.de/collection/catalogue/details/culture/DSM-22645
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| Zymomonas mobilis subsp. pomaceae Barker I DSM 22645 | 1.0.0 | 5.2.0 | fast | hac | NA | sup | NA | mods | pod5 |
| Zymomonas mobilis subsp. pomaceae Barker I DSM 22645 | 0.8.2 | 5.0.0 | fast | hac | NA | sup | NA | mods | pod5 |
You find a description of this sample here: https://www.dsmz.de/collection/catalogue/details/culture/DSM-2661
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| Methanocaldococcus jannaschii JAL-1 DSM 2661 | 1.0.0 | 5.2.0 | fast | hac | NA | sup | NA | mods | pod5 |
| Methanocaldococcus jannaschii JAL-1 DSM 2661 | 0.8.2 | 5.0.0 | fast | hac | NA | sup | NA | mods | pod5 |
You find a description of this sample here: https://www.dsmz.de/collection/catalogue/details/culture/DSM-6575
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| Sphaerotilus natans 6 DSM 6575 | 1.0.0 | 5.2.0 | fast | hac | NA | sup | NA | mods | pod5 |
| Sphaerotilus natans 6 DSM 6575 | 0.8.2 | 5.0.0 | fast | hac | NA | sup | NA | mods | pod5 |
You find a description of this sample here: https://www.dsmz.de/collection/catalogue/details/culture/DSM-6589
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| Thermanaerovibrio acidaminovorans Su883 DSM 6589 | 1.0.0 | 5.2.0 | fast | hac | NA | sup | NA | mods | pod5 |
| Thermanaerovibrio acidaminovorans Su883 DSM 6589 | 0.8.2 | 5.0.0 | fast | hac | NA | sup | NA | mods | pod5 |
You find a description of this sample here: https://zymoresearch.eu/products/zymobiomics-gut-microbiome-standard
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| ZymoGut | 1.0.0 | 5.2.0 | NA | NA | NA | NA | NA | mods | pod5 |
| ZymoGut | 0.8.2 | 5.0.0 | fast | hac | NA | sup | NA | mods | pod5 |
You find a description of this sample here: https://zymoresearch.eu/products/zymobiomics-hmw-dna-standard
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| ZymoHMW | 1.0.0 | 5.2.0 | fast | hac | NA | sup | NA | mods | pod5 |
| ZymoHMW | 0.7.3 | 5.0.0 | fast | hac | hacdup | sup | supdup | mods | pod5 |
| ZymoHMW | 1.0.0 | 5.0.0 | NA | NA | NA | NA | NA | NA | pod5 |
You find a description of this sample here: https://zymoresearch.eu/products/zymobiomics-oral-microbiome-standard
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| ZymoOral | 1.0.0 | 5.2.0 | NA | NA | NA | NA | NA | mods | pod5 |
| ZymoOral | 0.8.2 | 5.0.0 | fast | hac | NA | sup | NA | mods | pod5 |
You find a description of this sample here: https://zymoresearch.eu/collections/zymobiomics-microbial-community-standards/products/zymobiomics-fecal-reference-with-trumatrix-technology
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| ZymoFecal | 1.0.0 | 5.2.0 | NA | NA | NA | NA | NA | mods | pod5 |
| ZymoFecal | 0.7.3 | 5.0.0 | NA | NA | NA | NA | NA | mods | pod5 |
| ZymoFecal | 0.8.2 | 5.0.0 | fast | hac | NA | sup | NA | mods | pod5 |
You find a description of this sample here: wwtp_NL-09
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| wwtp_NL-09 | 1.0.0 | 5.2.0 | NA | NA | NA | NA | NA | mods | NA |
You find a description of this sample here: wwtp_IL-01
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| wwtp_IL-01 | 1.0.0 | 5.2.0 | NA | NA | NA | NA | NA | mods | NA |
You find a description of this sample here: wwtp_US2-26
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| wwtp_US2-26 | 1.0.0 | 5.2.0 | NA | NA | NA | NA | NA | mods | NA |
You find a description of this sample here: wwtp_IN-06
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| wwtp_IN-06 | 1.0.0 | 5.2.0 | NA | NA | NA | NA | NA | mods | NA |
You find a description of this sample here: wwtp_US1-124
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| wwtp_US1-124 | 1.0.0 | 5.2.0 | NA | NA | NA | NA | NA | mods | NA |
You find a description of this sample here: https://github.com/cmc-aau/mfd_metadata/blob/main/analysis/releases/latest_mfd_db.xlsx
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| sediment_MFD04716 | 1.0.0 | 5.2.0 | NA | NA | NA | NA | NA | mods | NA |
You find a description of this sample here: https://github.com/cmc-aau/mfd_metadata/blob/main/analysis/releases/latest_mfd_db.xlsx
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| sediment_MFD00905 | 1.0.0 | 5.2.0 | NA | NA | NA | NA | NA | mods | NA |
You find a description of this sample here: https://github.com/cmc-aau/mfd_metadata/blob/main/analysis/releases/latest_mfd_db.xlsx
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| sediment_MFD05674 | 1.0.0 | 5.2.0 | NA | NA | NA | NA | NA | mods | NA |
You find a description of this sample here: https://github.com/cmc-aau/mfd_metadata/blob/main/analysis/releases/latest_mfd_db.xlsx
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| sediment_MFD10007 | 1.0.0 | 5.2.0 | NA | NA | NA | NA | NA | mods | NA |
You find a description of this sample here: https://github.com/cmc-aau/mfd_metadata/blob/main/analysis/releases/latest_mfd_db.xlsx
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| sediment_MFD09779 | 1.0.0 | 5.2.0 | NA | NA | NA | NA | NA | mods | NA |
You find a description of this sample here: https://github.com/cmc-aau/mfd_metadata/blob/main/analysis/releases/latest_mfd_db.xlsx
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| soil_MFD00392 | 1.0.0 | 5.2.0 | NA | NA | NA | NA | NA | mods | NA |
You find a description of this sample here: https://github.com/cmc-aau/mfd_metadata/blob/main/analysis/releases/latest_mfd_db.xlsx
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| soil_MFD06742 | 1.0.0 | 5.2.0 | NA | NA | NA | NA | NA | mods | NA |
You find a description of this sample here: https://github.com/cmc-aau/mfd_metadata/blob/main/analysis/releases/latest_mfd_db.xlsx
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| soil_MFD06229 | 1.0.0 | 5.2.0 | NA | NA | NA | NA | NA | mods | NA |
You find a description of this sample here: https://github.com/cmc-aau/mfd_metadata/blob/main/analysis/releases/latest_mfd_db.xlsx
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| soil_MFD02242 | 1.0.0 | 5.2.0 | NA | NA | NA | NA | NA | mods | NA |
You find a description of this sample here: https://github.com/cmc-aau/mfd_metadata/blob/main/analysis/releases/latest_mfd_db.xlsx
| Sample | dorado version | basecall model version | fast | hac | hacdup | sup | supdup | mods | pod5 |
|---|---|---|---|---|---|---|---|---|---|
| soil_MFD02360 | 1.0.0 | 5.2.0 | NA | NA | NA | NA | NA | mods | NA |