title: EUPAN enables pan-genome studies of a large number of eukaryotic genomes.
abstract: CONCLUSIONS
  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.
  
  
  METHODS
  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 .
  
  
  BACKGROUND
  ccwei@sjtu.edu.cn or jianxin.shi@sjtu.edu.cn.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.|Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Pudong District, Shanghai 201203, China.
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Hu
authors.affiliation: Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.|Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Pudong District, Shanghai 201203, China.
authors.forename: Chen
authors.initials: C
authors.lastname: Sun
authors.affiliation: Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Kuang-Chen
authors.initials: KC
authors.lastname: Lu
authors.affiliation: Bio-X Institutes, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Xixia
authors.initials: X
authors.lastname: Chu
authors.affiliation: Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Yue
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.|Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Pudong District, Shanghai 201203, China.
authors.forename: Jinyuan
authors.initials: J
authors.lastname: Lu
authors.affiliation: Department of Genetic and Developmental Science, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
authors.forename: Jianxin
authors.initials: J
authors.lastname: Shi
authors.affiliation: Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.|Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Pudong District, Shanghai 201203, China.
authors.forename: Chaochun
authors.initials: C
authors.lastname: Wei
mesh_terms: D056890:Eukaryota / Q000235:genetics*; D005828:Genetics, Population / Q000379:methods*; D016678:Genome; D023281:Genomics / Q000379:methods; D060005:Genotyping Techniques / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software