A searchable and exportable tab-separated table of the following metadata is now available.
🔹 italics = potential considerations
| metadata | definition | reference of definition[<url_to_definition>] | expected unit of measurement | examples | source |
|---|---|---|---|---|---|
| sample_name | A local identifier or name that for the material sample used for extracting nucleic acids, and subsequent sequencing. It can refer either to the original material collected or to any derived sub-samples. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. INSDC requires every sample name from a single Submitter to be unique. | MIXS:0001107 | free text with identifier | e.g. ISDsoil1 | GSC MIxS/MIGS Bacteria (“GSC MIXS: MIGSBacteria”) |
| seq_meth | Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103) | MIXS:0000050 | <name_of_seq_machine>[ontology] | e.g. 454 Genome Sequencer FLX [OBI:0000702] | GSC MIxS/MIGS Bacteria (“GSC MIXS: MIGSBacteria”), ENA Metadata Validation: Instrument (“ENA Metadata Validation: Instrument”) |
| lib_source | The lib_source specifies the type of source material that is being sequenced | Link to permitted values | Free text from selected list of values | e.g. METAGENOMIC. | ENA Metadata Validation: Source (“ENA Metadata Validation: Source”) |
| lib_strategy | Sequencing technique intended for this library | Link to permitted values | Free text from selected list of values | e.g. WGS, WGA, 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 | Link to permitted values | Free text from selected list of values | e.g. RANDOM, cDNA_oligo_dT etc. | ENA Metadata Validation: Selection (“ENA Metadata Validation: Selection”) |
| nucl_acid_ext | Literature reference or SOP describing nucleic extraction | MIXS:0000037 | Free text to the reference | e.g. CTAB extraction, Phenol-Cloroform Extraction | GSC MIxS/MIGS Bacteria (“GSC MIXS: MIGSBacteria”) |
| 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 | MIXS:0000038 | PMID, DOI, URL | e.g. https://phylogenomics.me/protocols/16s-pcr-protocol/ | GSC MISAG [gsc_migs_bacteria] |
| sequence_count | Number of reads in the library (sequencing depth), assigned at submission | Link to submission of genomes | integer value + unit of measurement | e.g. 32,283,453 OR 32.3M | Adapted from NCBI-SRA (Leinonen et al. 2011) |
| basepairs_count | Number of base pairs (nucleotides) in the library, assigned at submission | Link to submission of genomes | integer value + unit of measurement | e.g. 6,400,000 or 6.4M | Adapted from NCBI-SRA (Leinonen et al. 2011) |
| average_length (optional) | basepairs_count divided by sequence_count | As defined here | Integer | e.g. 198 | Calculated as basepairs_count/sequence_count |
| sequence_q30 (optional) | Percentage of reads in the library (sequencing depth) with quality above 30 | Link to resource to calculate | Integer from 0-100 | e.g. 85 | SRA-Tinder (NCBI Hackathons) |
| basepairs_q30 (optional) | Percentage of base pairs (nucleotides) in the library with quality above 30 | Link to resource to calculate | Integer from 0-100 | e.g. 80 | SRA-Tinder (NCBI Hackathons) |
| checksum | Hash value for data integrity | Link to ENA MD5 Checksum | string with checksum | e.g. MD5: cbc41d0e49636872a765b950cb7f410a | Data transfer and data integrity |
| metadata | definition | reference of definition[<url_to_definition>] | expected unit of measurement | example | source |
|---|---|---|---|---|---|
| run_ref | Accessions/identifiers linking to the raw data (FASTQ) | Link to reference | run_accession in the format SRR, ERR or DRR | e.g. RUN_REF 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 genome | MIXS:0000053 | free text | e.g. 16s rRNA gene, multi-marker approach, other | GSC MIXS: MIMAG (“GSC MIXS: MIMAG”) |
| assembly_qual | The assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the large subunit (LSU) RNA, small subunit (SSU) and the presence of 5.8S rRNA or 5S rRNA depending on whether it is a eukaryotic or prokaryotic genome, respectively. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated | MIXS:0000056 | free text from predetermined strings | e.g. Medium Quality Draft | GSC MIxS/MIGS Bacteria (“GSC MIXS: MIGSBacteria”) |
| assembly_software | Tool(s) used for assembly, including version number and parameters | MIXS:0000058 | free text | e.g. metaSPAdes (3.11.0);kmer set 21,33,55,77,99,121, default parameters otherwise | GSC MIxS/MIGS Bacteria (“GSC MIXS: MIGSBacteria”) |
| 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. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores | MIXS:0000069 | integer value (%) | e.g. med; 60% | GSC MIXS: MIMAG (“GSC MIXS: MIMAG”) |
| compl_software | Tools used for completion estimate | MIXS:0000070 | free text string | e.g. checkm (v1.1.6) | GSC MIXS: MIMAG (“GSC MIXS: MIMAG”) |
| contam_score | The contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases. | MIXS:0000072 | integer value (%) | e.g. 0.01 | GSC MIXS: MIMAG (“GSC MIXS: MIMAG”) |
| mag_cov_software | Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets | MIXS:0000080 | Free text | e.g. bbmap | GSC MIXS: MIMAG (“GSC MIXS: MIMAG”) |
| bin_software | Tool(s) used for the extraction of genomes from metagenomic datasets, where possible include a product ID (PID) of the tool(s) used | MIXS:0000078 | Free text | e.g. MaxBin 2.0 (https://doi.org/10.1093/bioinformatics/btv638) | GSC MIXS: MIMAG (“GSC MIXS: MIMAG”) |
| bin_param | The parameters that have been applied during the extraction of genomes from metagenomic datasets | MIXS:0000077 | Free text | e.g. kmer, coverage, etc | GSC MIXS: MIMAG (“GSC MIXS: MIMAG”) |
| coverage | The estimated depth of sequencing coverage | Link to usecase | integer value | 30.5 | ENA Submitting Metagenome Assemblies (“ENA Submitting Metagenome Assemblies”) |
| number_contig | Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG | MIXS:0000060 | integer value | e.g. 40 | GSC MIxS/MIGS Bacteria (“GSC MIXS: MIGSBacteria”), Roadmap for naming uncultivated Archaea and Bacteria (Murray et al. 2020) |
| N50 | The length of the shortest contig representing half of the assembly length | Link to reference 1 Link to reference 2 | integer value + unit | e.g. N50=4kb | Roadmap for naming uncultivated Archaea and Bacteria (Murray et al. 2020) |
| x16s_recover (optional) | Can a 16S gene be recovered from the submitted sequence | MIXS:0000065 | free text string | e.g. yes | Adapted from GSC MIXS: MIMAG (“GSC MIXS: MIMAG”) |
| x16s_recover_software (optional) | Tools used for 16S rRNA gene extraction | MIXS:0000066 | free text string | e.g. rambl (v2); default parameters | Adapted from GSC MIXS: MIMAG (“GSC MIXS: MIMAG”) |
| trnas (optional) | Total number of tRNAs identified from the genome | MIXS:0000067 | integer value | e.g. 18 | GSC MIXS: MIMAG (“GSC MIXS: MIMAG”), Roadmap for naming uncultivated Archaea and Bacteria (Murray et al. 2020) |
| trna_ext_software (optional) | Tools used for tRNA identification | MIXS:0000068 | free text string | e.g. infernal (v2); default parameters | GSC MIXS: MIMAG (“GSC MIXS: MIMAG”) |
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: MIGSBacteria.” https://genomicsstandardsconsortium.github.io/mixs/MIGSBacteria/.
“GSC MIXS: MIMAG.” https://genomicsstandardsconsortium.github.io/mixs/MIMAG/.
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.
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.
Rocca-Serra, Philippe, Alasdair J G Gray, Alejandra Delfin Rossaro, Andrea Splendiani, Andrea Zaliani, Andreas Pippow, Anne Cambon-Thomsen, et al. 2022. “The FAIR Cookbook.” https://github.com/FAIRplus/the-fair-cookbook/.
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.
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| 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: MIMAG (“GSC MIXS: MIMAG”) |
| assembly_qual | Assembly quality category | e.g. Medium Quality Draft | GSC MIxS/MIGS Bacteria (“GSC MIXS: MIGSBacteria”) |
| 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 Bacteria (“GSC MIXS: MIGSBacteria”) |
| coverage | The estimated depth of sequencing coverage (in x) | ENA Submitting Metagenome Assemblies (“ENA Submitting Metagenome Assemblies”) | |
| number_contig | Total number of contigs | e.g. 40 | GSC MIxS/MIGS Bacteria (“GSC MIXS: MIGSBacteria”), Roadmap for naming uncultivated Archaea and Bacteria (Murray et al. 2020) |
| LSU_recover | Detection of the 23S rRNA (BA) or 5.8S/28S rRNA (E) | e.g. yes | Adapted from GSC MIXS: MIMAG (“GSC MIXS: MIMAG”) |
| LSU_recover_software | Tools for LSU extraction | Adapted from GSC MIXS: MIMAG (“GSC MIXS: MIMAG”) | |
| SSU_recover | Detection of the 16S rRNA (BA) or 18S rRNA (E) | e.g. yes | Adapted from GSC MIXS: MIMAG (“GSC MIXS: MIMAG”) |
| SSU_recover_software | Tools for SSU extraction | e.g. rambl (v2); default parameters | Adapted from GSC MIXS: MIMAG (“GSC MIXS: MIMAG”) |
| trnas | Total number of tRNAs identified from the MAG | e.g. 18 | GSC MIXS: MIMAG (“GSC MIXS: MIMAG”), 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: MIMAG (“GSC MIXS: MIMAG”) |
| compl_score | Completeness score | e.g. med; 60% | GSC MIXS: MIMAG (“GSC MIXS: MIMAG”) |
| compl_software | Tools used for completion estimate | e.g. checkm (v1.1.6) | GSC MIXS: MIMAG (“GSC MIXS: MIMAG”) |
| contam_score | Contamination score | e.g. 0.01 | GSC MIXS: MIMAG (“GSC MIXS: MIMAG”) |
| contam_software | Tool(s) used in contamination screening | e.g. checkm (v1.1.6) | GSC MIXS: MIMAG (“GSC MIXS: MIMAG”) |
| Comments/questions: |
|---|
| Is coverage factored into completeness? If not, it seems we should consider separating genome coverage and sequence depth -NME 27APR22 |
| We need a reference for a consensual definitions of these terms to avoid confusion -CP 17JUL22 |
| Took the definitions from ENA Submitting Metagenome Asseblies, replaced coverage and depth with one definition -MB 11AUG23 |
OBS: THE MIM FOR FASTA METAGENOME HAVE TO BE FURTHER DISCUSSED IF NEEDED OR IF IT SHOULD BE MERGED IN A DIFFERENT CATEGORY.