Naming Scheme

The constraints are:

  • Naming should be stable: it should never change. This implies that enough room should be given to account for many years of future samples
  • Name should be informative: one should get an idea of where the gene/SAG comes from from its name.
  • Name should be concise: ideally, a gene name (which is the end product in a way) should be kept under 20 characters

Quick guide:

sample well asbly reserved
_____  ___  _     _
     –    –  –––––
 plate    run gene

Complete description

  • Sample:
    • Five characters, alphanumeric, letter in capitals
    • Should be as informative as possible (e.g. O331A for Ocean Drilling program exp. 331, sample A)
  • Plates:
    • Start with sample ID
    • One extra character (A-Z) to indicate the nth plate from this sample (e.g. O331AC for the third plate sorted from sample O331A)
    • The same extra character (a-z and 0-9) for plate dilutions (e.g. O331Ab for the second plate dilution from sample O331A)
    • For metagenomes, this should indicate different extractions from the same sample.
  • Well/Metagenome/Pure culture/Amplicons:
    • Starts with plate ID, then an underscore
    • Three characters in addition: one letter (A-L) and two digits (00-16) to describe the well.
    • Metagenomes are labeled with X, then 01. Further digits are reserved for later use.
    • Pure cultures are labeled with Z, then 01. Further digits are reserved for later use.
    • Amplicons are labeled with Y, then 01. Further digits are reserved for later use.
    • A1 should be always written A01
    • E.g. O331AC_C09
  • DNA library
    • Describes many DNA libraries from the same source: can be different dilution plates, different sequencing runs, different preparations, for example.
    • Starts with the well ID
    • One character (A-Z; 0-9), in order
    • E.g. O331AC_C09A
  • Assembly
    • Describes one assembly performed on one dataset from one run (SAG)
    • Starts with run ID, then an underscore
    • One character (A-Z; 0-9), in order
    • E.g. O331AC_C09A_B
  • Genes:
    • Starts with assembly ID
    • 6 digits, with a 10 increment to allow adding genes in the middle
    • tRNAs have t prefix, rRNAs a r instead of the first digit
    • E.g. O331AC_C09A_B002340, O331AC_C09A_Bt05610