PatMaN: rapid alignment of short sequences to large databases. - Kay Prüfer; Udo Stenzel; Michael Dannemann; Richard E. Green; Michael Lachmann; Janet Kelso (Bioinform., 2008)

freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers. - Gabriel Renaud; Martin Kircher; Udo Stenzel; Janet Kelso (Bioinform., 2013)

deML: robust demultiplexing of Illumina sequences using a likelihood-based approach. - Gabriel Renaud; Udo Stenzel; Tomislav Maricic; Victor Wiebe; Janet Kelso (Bioinform., 2015)