added 104 characters in body
Source Link
gringer
  • 10.9k
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  • 17
  • 66

I would say that the following metrics are useful:

  • Sample source (Extraction place, person, date)
  • Details about pre-HTS preparation (e.g. amplicon PCR, rRNA removal)
  • Reads per sample (+ per barcode / lane, if available)
  • Sequencing kit (e.g. TruSeq v3), useful for adapter trimming
  • Sequence length (e.g. 125bp)
  • Paired end / single end
  • If paired end, target fragment length in sample prep (e.g. 650bp)
  • Reference sequence metadata
    • Scientific name
    • Location of reference genome (preferably a stable web address)
    • Version of reference genome
    • Read mapping rate (per sample / barcode / lane), as a percentage of total reads
    • Mapping program + version
  • If available, potential contaminating organisms
    • Name / description
    • Location of contaminant sequence (preferably a stable web address)
    • Estimated mapping rate (bearing in mind that there may be some overlap with the target)
    • Mapping program + version

More generally, ENA / EBI has an excellent reference in sample checklists, which indicate the minimum acceptable metadata for attaching to sequence archive data:

https://www.ebi.ac.uk/ena/submit/checklists

I would say that the following metrics are useful:

  • Sample source
  • Reads per sample (+ per barcode / lane, if available)
  • Sequencing kit (e.g. TruSeq v3), useful for adapter trimming
  • Sequence length (e.g. 125bp)
  • Paired end / single end
  • If paired end, target fragment length in sample prep (e.g. 650bp)
  • Reference sequence metadata
    • Scientific name
    • Location of reference genome (preferably a stable web address)
    • Version of reference genome
    • Read mapping rate (per sample / barcode / lane), as a percentage of total reads
    • Mapping program + version
  • If available, potential contaminating organisms
    • Name / description
    • Location of contaminant sequence (preferably a stable web address)
    • Estimated mapping rate (bearing in mind that there may be some overlap with the target)
    • Mapping program + version

More generally, ENA / EBI has an excellent reference in sample checklists, which indicate the minimum acceptable metadata for attaching to sequence archive data:

https://www.ebi.ac.uk/ena/submit/checklists

I would say that the following metrics are useful:

  • Sample source (Extraction place, person, date)
  • Details about pre-HTS preparation (e.g. amplicon PCR, rRNA removal)
  • Reads per sample (+ per barcode / lane, if available)
  • Sequencing kit (e.g. TruSeq v3), useful for adapter trimming
  • Sequence length (e.g. 125bp)
  • Paired end / single end
  • If paired end, target fragment length in sample prep (e.g. 650bp)
  • Reference sequence metadata
    • Scientific name
    • Location of reference genome (preferably a stable web address)
    • Version of reference genome
    • Read mapping rate (per sample / barcode / lane), as a percentage of total reads
    • Mapping program + version
  • If available, potential contaminating organisms
    • Name / description
    • Location of contaminant sequence (preferably a stable web address)
    • Estimated mapping rate (bearing in mind that there may be some overlap with the target)
    • Mapping program + version

More generally, ENA / EBI has an excellent reference in sample checklists, which indicate the minimum acceptable metadata for attaching to sequence archive data:

https://www.ebi.ac.uk/ena/submit/checklists

Source Link
gringer
  • 10.9k
  • 3
  • 17
  • 66

I would say that the following metrics are useful:

  • Sample source
  • Reads per sample (+ per barcode / lane, if available)
  • Sequencing kit (e.g. TruSeq v3), useful for adapter trimming
  • Sequence length (e.g. 125bp)
  • Paired end / single end
  • If paired end, target fragment length in sample prep (e.g. 650bp)
  • Reference sequence metadata
    • Scientific name
    • Location of reference genome (preferably a stable web address)
    • Version of reference genome
    • Read mapping rate (per sample / barcode / lane), as a percentage of total reads
    • Mapping program + version
  • If available, potential contaminating organisms
    • Name / description
    • Location of contaminant sequence (preferably a stable web address)
    • Estimated mapping rate (bearing in mind that there may be some overlap with the target)
    • Mapping program + version

More generally, ENA / EBI has an excellent reference in sample checklists, which indicate the minimum acceptable metadata for attaching to sequence archive data:

https://www.ebi.ac.uk/ena/submit/checklists