Abbreviate strings to short unique identifiers

For each string in a set of strings, determine a unique tag that is a substring of fixed size k unique to that string, if it has one. If no such unique substring exists, the least frequent substring is used. If multiple unique substrings exist, the lexicographically smallest substring is used. This lexicographically smallest substring of size k is called the uniqtag of that string.


Command line program

curl -o ~/bin/uniqtag https://raw.githubusercontent.com/sjackman/uniqtag/master/uniqtag
chmod +x ~/bin/uniqtag

or using Homebrew or Linuxbrew

brew install uniqtag

R package

# install.packages("devtools")


Shaun D. Jackman, Joerg Bohlmann, İnanç Birol (2014) UniqTag: Content-derived unique and stable identifiers for gene annotation. bioRxiv, doi:10.1101/007583.


When working on an ongoing genome sequencing and assembly project, it is rather inconvenient when gene identifiers change from one build of the assembly to the next. The gene labelling system described here, UniqTag, addresses this common challenge. UniqTag assigns a unique identifier to each gene that is a representative k-mer, a string of length k, selected from the sequence of that gene. Unlike serial numbers, these identifiers are stable between different assemblies and annotations of the same data without requiring that previous annotations be lifted over by sequence alignment. We assign UniqTag identifiers to nine builds of the Ensembl human genome spanning seven years to demonstrate this stability.