Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. - Felix Krueger; Simon R. Andrews (Bioinform., 2011)

B-SOLANA: an approach for the analysis of two-base encoding bisulfite sequencing data. - Benjamin Kreck; George Marnellos; Julia Richter; Felix Krueger; Reiner Siebert; Andre Franke (Bioinform., 2012)

Cluster Flow: A user-friendly bioinformatics workflow tool. - Philip Ewels; Felix Krueger; Max Käller; Simon R. Andrews (F1000Research, 2016)