ppsPCP: a plant presence/absence variants scanner and pan-genome construction pipeline.
basic_science · Level V
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- Record sourced from PubMed, PMID 30851098.
- Also identified by DOI 10.1093/bioinformatics/btz168.
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Abstract
Since the idea of pan-genomics emerged several tools and pipelines have been introduced for prokaryotic pan-genomics. However, not a single comprehensive pipeline has been reported which could overcome multiple challenges associated with eukaryotic pan-genomics. To aid the eukaryotic pan-genomic studies, here we present ppsPCP pipeline which is designed for eukaryotes especially for plants. It is capable of scanning presence/absence variants (PAVs) and constructing a fully annotated pan-genome. We believe with these unique features of PAV scanning and building a pan-genome together with its annotation, ppsPCP will be useful for plant pan-genomic studies and aid researchers to study genetic/phenotypic variations and genomic diversity. The ppsPCP is freely available at github DOI: https://doi.org/10.5281/zenodo.2567390 and webpage http://cbi.hzau.edu.cn/ppsPCP/. Supplementary data are available at Bioinformatics online.
Medical subject headings
- Genome, Plant
- Software