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pibase is a command-line tool to validate single nucleotide polymorphism (SNP) in diploid and haploid genomes, exome data, and in targeted enrichment data. The pibase algorithm works by extracting features at specified coordinates in alignment files and identifies reproducible genotypes.


DNA polymorphism; Comparative genomics; Phylogenetics


  • Operation: Nucleic acid sequence analysis; SNP detection
  • Software interface: Command-line user interface
  • Language: Python
  • Operating system: Linux
  • License: Not stated
  • Cost: Free for non commercial usage.
  • Version name: 1.4.7
  • Credit: The German Ministry of Education and Research (BMBF); the National Genome Research Network (NGFN); the Deutsche Forschungsgemeinschaft (DFG) Cluster of Excellence ‘Inflammation at Interfaces’; EU Seventh Framework Programme [FP7/2007-2013, grant number 201418, READNA and 262055, ESGI]. Funding for open access charge: EU [FP7/2007-2013, grant number 201418].
  • Contact: Michael Forster m.forster _at_ | Andre Franke a.franke _at_
  • Collection: -


Forster M, Forster P, Elsharawy A, Hemmrich G, Kreck B, Wittig M, Thomsen I, Stade B, Barann M, Ellinghaus D, Petersen BS, May S, Melum E, Schilhabel MB, Keller A, Schreiber S, Rosenstiel P, Franke A "From next-generation sequencing alignments to accurate comparison and validation of single-nucleotide variants: the pibase software." Nucleic Acids Res. 2013 Jan 7;41(1):e16.
PMID: 22965131
PMCID: PMC3592472

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