A searchable and exportable tab-separated table of the following metadata is now available.
🔹 italics = potential considerations
| metadata | definition | examples | source |
|---|---|---|---|
| sample_name | Identifier of the sample | e.g. ISDsoil1 | GSC MIxS/MIGS Bacteria (“GSC MIXS: MIGSBacteria”) |
| seq_meth | Sequencing method used | e.g. 454 Genome Sequencer FLX [OBI:0000702] | GSC MIxS/MIGS Bacteria (“GSC MIXS: MIGSBacteria”), 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 Bacteria (“GSC MIXS: MIGSBacteria”) |
| 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”) |
| nucl_acid_ext | Literature reference or SOP describing nucleic extraction | e.g. CTAB extraction, Phenol-Cloroform Extraction | The FAIR Cookbook (Rocca-Serra et al. 2022) |
| nucl_acid_ext_treat | Treatment of nucleic acid after extraction | e.g. DNase, RNase | Adapted from The FAIR Cookbook (Rocca-Serra et al. 2022) |
| 🔹 insert_length | for inner dist. calc. (or incl. in lib_layout?)(Array Express parameter: insert “Nominal Length” | ||
| 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) | |
| quality_score | Q30, quality above 30 | e.g. 49 | SRA-Tinder (NCBI Hackathons) |
| checksum | Hash value for data integrity | e.g. MD5: cbc41d0e49636872a765b950cb7f410a | Data transfer and data integrity |
| 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 |
## Minimal technical metadata for
Metagenome Assembled Genome (MAG) FASTA file
| 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) |
| N50 | The length of the shortest contig representing half of the assembly length | 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: |
|---|
| Not sure to understand what is the source metadata -CP 17JUL22 |
| As far as I understand that would be the same as run_ref i.e. raw data that was used to recover the MAG -MB 10AUG23 |
| Took the definitions from ENA Submitting Metagenome Asseblies, depth with coverage, removed source as it should be the same thing as run_ref -MB 11AUG23 |
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), and Roadmap for naming uncultivated Archaea and Bacteria (Murray et al. 2020) can be found online. We also highly encourage the readers of this GitHub to read The FAIR cookbook recipes (Rocca-Serra et al. 2022).
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.