We describe a rapid algorithm for demultiplexing DNA sequence reads with in-read indices. Axe selects the optimal index present in a sequence read, even in the presence of sequencing errors. The algorithm is able to handle combinatorial indexing, indices of differing length and several mismatches per index sequence.

Availability and implementation

Axe is implemented in C, and is used as a command-line program on Unix-like systems. Axe is available online at, and is available in Debian/Ubuntu distributions of GNU/Linux as the package axe-demultiplexer.

Supplementary information

Supplementary data are available at Bioinformatics online

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