What sequencing data metrics should I record? 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.
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