| metadata | definition | examples | source |
|---|---|---|---|
| sample_name | Identifier of the sample | e.g. ISDsoil1 | GSC MIxS/MIGS Miuvig (“Miuvig”) |
| seq_meth | Sequencing method used | e.g. 454 Genome Sequencer FLX OBI:0000702 | GSC MIxS/MIGS Miuvig (“Miuvig”), ENA Metadata Validation: Instrument (“ENA Metadata Validation: Instrument”) |
| lib_layout | Specify whether to expect single, paired, or other configuration of reads | e.g. single-end, paired end or others | GSC MIxS/MIGS Miuvig (“Miuvig”) |
| lib_source | The lib_source specifies the type of source material that is being sequenced | e.g. genomic, metagenomic, transcriptomic, etc. | ENA Metadata Validation: Source (“ENA Metadata Validation: Source”) |
| lib_strategy | Sequencing technique intended for this library | e.g. WGS, Amplicon, etc. | ENA Metadata Validation: Strategy (“ENA Metadata Validation: Strategy”) |
| lib_selection | Whether any method was used to select and/or enrich the material being sequenced | e.g. Random, PCR, etc. | ENA Metadata Validation: Selection (“ENA Metadata Validation: Selection”) |
| sequence_count | Number of reads in the library (sequencing depth) or ‘spots’ | e.g. 32,283,453 | Adapted from NCBI-SRA (Leinonen et al. 2011) |
| basepairs_count | Number of base pairs (nucleotides) in the library or ‘bases’ | e.g. 6,400,000,000 | Adapted from NCBI-SRA (Leinonen et al. 2011) |
| average_length | As basepairs_count divided by sequence_count | e.g. 198 | Calculated as basepairs_count/sequence_count |
| sequence_count_qual | Number of reads in the library (sequencing depth) after quality filtering | SRA-Tinder (NCBI Hackathons) | |
| basepairs_count_qual | Number of base pairs (nucleotides) in the library after quality filtering | SRA-Tinder (NCBI Hackathons) | |
| checksum | Hash value for data integrity | e.g. MD5: cbc41d0e49636872a765b950cb7f410a | Data transfer and data integrity |
| nucl_acid_amp | A link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids | https://phylogenomics.me/protocols/16s-pcr-protocol/ | GSC MIxS/MIGS Miuvig (“Miuvig”) |
| Comments/questions: |
|---|
| Should we also add nucl_ext_method and nucl_extr_treat here -MB 11AUG23 |
| metadata | definition | examples | source |
|---|---|---|---|
| run_ref | Accessions/identifiers linking to the raw data (FASTQ) | e.g. accession = “ERR178314” | Adapted from ENA (“ENA How to Submit Other Analyses: Submitting Read Alignments”) |
| tax_ident | The phylogenetic marker(s) used to assign an organism name to the SAG or MAG | e.g. 16s rRNA gene, multi-marker approach, other | GSC MIxS/MIGS Miuvig (“Miuvig”) |
| assembly_qual | The assembly quality category is based on sets of criteria outlined for each assembly quality category. | e.g. Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. | GSC MIxS/MIGS Miuvig (“Miuvig”) |
| assembly_software | Tool(s) used, version and parameters | e.g. metaSPAdes (3.11.0);kmer set 21,33,55,77,99,121, default parameters otherwise | GSC MIxS/MIGS Miuvig (“Miuvig”) |
| mag_cov_software | Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of uVIGs from metagenomic datasets | e.g. bbmap, bowtie, bwa, other | ENA Submitting Metagenome Assemblies (“ENA Submitting Metagenome Assemblies”) |
| vir_ident_software | Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used | e.g. VirSorter; 1.0.4; Virome database, category 2 | GSC MIxS/MIGS Miuvig (“Miuvig”) |
| number_contig | Total number of contigs in the cleaned/submitted assembly that makes up a given UViG | e.g. 40 | GSC MIxS/MIGS Miuvig (“Miuvig”), Roadmap for naming uncultivated Archaea and Bacteria (Murray et al. 2020) |
| N50 | The length of the shortest contig representing half of the assembly length | Roadmap for naming uncultivated Archaea and Bacteria (Murray et al. 2020) | |
| trnas | Total number of tRNAs identified from the MAG | e.g. 18 | GSC MIxS/MIGS Miuvig (“Miuvig”), Roadmap for naming uncultivated Archaea and Bacteria (Murray et al. 2020) |
| trna_ext_software | Tools used for tRNA identification | e.g. infernal (v2); default parameters | GSC MIxS/MIGS Miuvig (“Miuvig”) |
| compl_score | Completeness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. | e.g. med; 60% | GSC MIXS: MIMAG (“GSC MIXS: MIMAG”) |
| compl_software | Tools used for completion estimate | e.g. checkm (v1.1.6), anvi’o, busco | GSC MIxS/MIGS Miuvig (“Miuvig”) |
| source_uvig | Type of dataset from which the UViG was obtained | e.g. viral fraction metagenome (virome) | GSC MIxS/MIGS Miuvig (“Miuvig”) |
| pathogenicity | To what is the entity pathogenic | e.g. human, animal, plant, fungi, bacteria | GSC MIxS/MIGS Miuvig (“Miuvig”) |
The publications describing the reasons for formation of The minimum information about a genome sequence (MIGS) (Field et al. 2008), Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications (Yilmaz et al. 2011), Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea (Bowers et al. 2017), Minimum Information about an Uncultivated Virus Genome (MIUViG) (Roux et al. 2019) and Roadmap for naming uncultivated Archaea and Bacteria (Murray et al. 2020) can be found online.
Bowers, R., N. Kyrpides, R. Stepanauskas, et al. 2017. “Minimum Information about a Single Amplified Genome (MISAG) and a Metagenome-Assembled Genome (MIMAG) of Bacteria and Archaea.” Nat Biotechnol 35: 725–31. https://doi.org/10.1038/nbt.3893.
“ENA How to Submit Other Analyses: Submitting Read Alignments.” https://ena-docs.readthedocs.io/en/latest/submit/analyses/read-alignments.html.
“ENA Metadata Validation: Instrument.” https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#instrument.
“ENA Metadata Validation: Selection.” https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#selection.
“ENA Metadata Validation: Source.” https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#source.
“ENA Metadata Validation: Strategy.” https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#strategy.
“ENA Submitting Metagenome Assemblies.” https://ena-docs.readthedocs.io/en/latest/submit/assembly/metagenome.html.
Field, D., G. Garrity, T. Gray, N. Morrison, J. Selengut, P. Sterk, T. Tatusova, et al. 2008. “The Minimum Information about a Genome Sequence (MIGS) Specification.” Nature Biotechnology. 2008. https://doi.org/10.1038/nbt1360.
“GSC MIXS: MIMAG.” https://genomicsstandardsconsortium.github.io/mixs/0010011.
Leinonen, R., H. Sugawara, M. Shumway, and International Nucleotide Sequence Database Collaboration. 2011. “The Sequence Read Archive.” Nucleic Acids Research 39 (Database issue): D19–21. https://doi.org/10.1093/nar/gkq1019.
“Miuvig.” https://genomicsstandardsconsortium.github.io/mixs/0010012.
Murray, A. E., J. Freudenstein, S. Gribaldo, et al. 2020. “Roadmap for Naming Uncultivated Archaea and Bacteria.” Nat Microbiol 5: 987–94. https://doi.org/10.1038/s41564-020-0733-x.
NCBI Hackathons. “SRA-Tinder: A Tool to Discover Related Sequence Read Archive (SRA) Experiments.” https://github.com/NCBI-Hackathons/SRA_Tinder.
Roux, Simon, Evelien Adriaenssens, Bas Dutilh, and et al. 2019. “Minimum Information about an Uncultivated Virus Genome (MIUViG).” Nature Biotechnology 37: 29–37. https://doi.org/10.1038/nbt.4306.
Yilmaz, Pelin et al. 2011. “Minimum Information about a Marker Gene Sequence (MIMARKS) and Minimum Information about Any (x) Sequence (MIxS) Specifications.” Nature Biotechnology 29 (5): 415–20. https://doi.org/10.1038/nbt.1823.