A searchable and exportable tab-separated table of the following metadata is now available.
| 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 | 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”) |
| 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) | |
| target_gene | Targeted gene name for marker gene studies | e.g. 16S rRNA, ITS | GSC MIXS: MIMARKSSpecimen (“GSC MIXS: MIMARKSSpecimen”) |
| target_subfragment | Name of the targeted subregion | e.g. V3-V4, ITS1 | GSC MIXS: MIMARKSSpecimen (“GSC MIXS: MIMARKSSpecimen”) |
| pcr_primers | Forward and reverse primer sequences used | e.g. FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT | GSC MIXS: MIMARKSSpecimen (“GSC MIXS: MIMARKSSpecimen”) |
| checksum | Hash value for data integrity | e.g. MD5: cbc41d0e49636872a765b950cb7f410a | Data transfer and data integrity |
The publications describing the reasons for formation of The minimum information about a genome sequence (MIGS) (Field et al. 2008) and Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications (Yilmaz et al. 2011) can be found online.
“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.
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: MIMARKSSpecimen.” https://genomicsstandardsconsortium.github.io/mixs/MIMARKSSpecimen/.
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.
NCBI Hackathons. “SRA-Tinder: A Tool to Discover Related Sequence Read Archive (SRA) Experiments.” https://github.com/NCBI-Hackathons/SRA_Tinder.
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.