text: user167: I'm new to bioinformatics and Im starting a new microbial sequencing project and I'd like to record all of the qc data correctly. This is research and I'm not sure what I'll need later. Is there any consensus on useful qc metrics to record in a database for each sequencing run?
  No rnaseq, running FastQC, assembling with a defined reference for a single species. 
  
  user73: 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
  
original_text: 167: <p>I'm new to bioinformatics and Im starting a new microbial sequencing project and I'd like to record all of the qc data correctly. This is research and I'm not sure what I'll need later. Is there any consensus on useful qc metrics to record in a database for each sequencing run?</p>
  
  <p>No rnaseq, running FastQC, assembling with a defined reference for a single species. </p>
   73: <p>I would say that the following metrics are useful:</p>
  
  <ul>
  <li>Sample source (Extraction place, person, date)</li>
  <li>Details about pre-HTS preparation (e.g. amplicon PCR, rRNA removal)</li>
  <li>Reads per sample (+ per barcode / lane, if available)</li>
  <li>Sequencing kit (e.g. TruSeq v3), useful for adapter trimming</li>
  <li>Sequence length (e.g. 125bp)</li>
  <li>Paired end / single end</li>
  <li>If paired end, target fragment length in sample prep (e.g. 650bp)</li>
  <li>Reference sequence metadata
  
  <ul>
  <li>Scientific name</li>
  <li>Location of reference genome (preferably a stable web address)</li>
  <li>Version of reference genome</li>
  <li>Read mapping rate (per sample / barcode / lane), as a percentage of total reads</li>
  <li>Mapping program + version</li>
  </ul></li>
  <li>If available, potential contaminating organisms
  
  <ul>
  <li>Name / description</li>
  <li>Location of contaminant sequence (preferably a stable web address)</li>
  <li>Estimated mapping rate (bearing in mind that there may be some overlap with the target)</li>
  <li>Mapping program + version</li>
  </ul></li>
  </ul>
  
  <p>More generally, ENA / EBI has an excellent reference in sample checklists, which indicate the minimum acceptable metadata for attaching to sequence archive data:</p>
  
  <p><a href="https://www.ebi.ac.uk/ena/submit/checklists" rel="nofollow noreferrer">https://www.ebi.ac.uk/ena/submit/checklists</a></p>
  