MInAS Combinations
🛑 This draft is now deprecated due to changes in the structure of the MInAS project to better align with the MIxS infrastructure. Please see the latest drafts on the other pages in this section.
Version
The current version is: v0.0.2.
Warning
This can be considered a pre-alpha version, and has not been reviewed nor approved by the wider palaeogenomics community nor by the Genomics Standards Consortium.
The following submission combinations have been proposed by the SPAAM community to act as starting points for discussions. Not all types of ancient DNA research will currently be covered here, however the sub-fields should cover the vast majority of current research in the field. As the MInAS project develops, these default minimum-information submission combinations will be extended to include other areas.
All MInAS submission combinations will include the Ancient extension.
Note on typical archives
- ENA: EBI European Nucleotide Archive
- SRA: NCBI Sequence Read Archive
- MGnify: EBI Metagenomics
- GenBank: NCBI GenBank
| Category | Submission Combination | Palaeogenomics example | Typical Archive | Downloadable version |
|---|---|---|---|---|
| Reads | MimsHostAssociated + Ancient | Ancient human, animal, or plant reads (unmapped or mapped) | ENA/SRA | Click Here |
| Reads | MimsHostAssociated + Ancient | Ancient bacterial pathogen reads from skeletal material (unmapped or mapped) | ENA/SRA | Click Here |
| Reads | MimsHostAssociated + Ancient | Ancient virus pathogen reads from skeletal material (unmapped or mapped) | ENA/SRA | Click Here |
| Reads | MimsHostAssociated + Ancient | Ancient oral [dental calculus]; gut [palaeofaeces] microbiomes (reads) | ENA/SRA | Click Here |
| Reads | MimsHostAssociated + Ancient | Ancient any eukaryote or prokaryote from any skeletal or host-associated material | ENA/SRA | Click Here |
| Reads | SedimentMIMS + Ancient | Ancient any eukaryote or prokaryote reads from sediment (unmapped or mapped) | ENA/SRA | Click Here |
| Reads | SedimentMIMS + Ancient | Ancient human, animal, or plant reads from sediment (unmapped or mapped) | ENA/SRA | Click Here |
| Reads | SedimentMIMS + Ancient | Ancient bacterial pathogen reads from sediment (unmapped or mapped) | ENA/SRA | Click Here |
| Reads | SedimentMIMS + Ancient | Ancient virus pathogen reads from sediment (unmapped or mapped) | ENA/SRA | Click Here |
| Reads | SedimentMIMS + Ancient | sedaDNA (reads) | ENA/SRA | Click Here |
| Assembly | MimagHostAssociated + Ancient | Ancient pathogen [bacteria] (metagenomic de novo assembly) | MGnify | nan |
| Assembly | MimagHostAssociated + Ancient | Ancient pathogen [virus] (metagenomic de novo assembly) | MGnify | nan |
| Assembly | MimagHostAssociated + Ancient | Ancient pathogen [bacteria/virus]; oral [dental calculus] or gut [palaeofaeces] microbiomes (metagenomic de novo assembly) | MGnify | nan |
| Assembly | MimagSediment + Ancient | sedaDNA (metagenomic de novo assembly) | MGnify | nan |
| Genome | MigsBa(acteria)HostAssociated + Ancient | Ancient pathogen (assembled whole genome sequence) | GenBank | Click Here |
| Genome | MigsVi(rus)HostAssociated + Ancient | Ancient pathogen (assembled whole genome sequence) | GenBank | Click Here |
| Genome | MigsEu(karyote)HostAssociated + Ancient | Ancient human or animal genome or genome-wide data (assembled whole genome sequence) | GenBank | nan |
| Genome | MigsEu(karyote)PlantAssociated + Ancient | Ancient plant genome or genome-wide data (assembled whole genome sequence) | GenBank | nan |