What sequencing data metrics should I record?
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