For better experience, turn on JavaScript!

pibase
Home » Tools » SNP Tools » pibase

pibase

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.



pibase

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.

Topic

DNA polymorphism; Comparative genomics; Phylogenetics

Details

  • 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_ ikmb.uni-kiel.de | Andre Franke a.franke _at_ mucosa.de
  • Collection: -

Publications

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. https://doi.org/10.1093/nar/gks836
PMID: 22965131
PMCID: PMC3592472


Download and documentation







If you find errors, please report here.

SECTIONS

Tutorials
In-house software
Blog
News
Find Jobs
History
Definition of Bioinformatics
ENCYCLOPEDIA
COVID-19
⚬ Timeline of outbreak
⚬ Blog
⚬ Scientific Facts
⚬ Daily statistics
⚬ News


TOOLS


1. SNP Tools
2. GWAS Tools
3. Genotype Imputation Tools
4. MSA tools
5. CNV tools
6. WGA tools
7. RNA-seq tools
8. Proteomics Tools
9. Nucleic Acid Structure Analysis Tools
10. Nucleic Acid Sequence Analysis Tools
11. Sequence Logo Tools
12. In-house Software Tools

Find thousands of Bioinformatics and Life Science software tools and databases in the newly launched




Ads