LAUSR

Summary: Pan‐genome analyses are routinely carried out for bacteria to interpret the within‐species gene presence/absence variations (PAVs). However, pan‐genome analyses are rare for eukaryotes due to the large sizes and higher complexities of their genomes. Here we proposed EUPAN, a eukaryotic pan‐genome analysis toolkit, enabling automatic large‐scale eukaryotic pan‐genome analyses and detection of gene PAVs at a relatively low sequencing depth. In the previous studies, we demonstrated the effectiveness and high accuracy of EUPAN in the pan‐genome analysis of 453 rice genomes, in which we also revealed widespread gene PAVs among individual rice genomes. Moreover, EUPAN can be directly applied to the current re‐sequencing projects primarily focusing on single nucleotide polymorphisms. Availability and Implementation: EUPAN is implemented in Perl, R and C ++. It is supported under Linux and preferred for a computer cluster with LSF and SLURM job scheduling system. EUPAN together with its standard operating procedure (SOP) is freely available for non‐commercial use (CC BY‐NC 4.0) at http://cgm.sjtu.edu.cn/eupan/index.html. Contact: [email protected] or [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.