ArticleApplications in plant sciences2018
Fluidigm2PURC: Automated processing and haplotype inference for double-barcoded PCR amplicons.
Article in Applications in plant sciences, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed, 15 citations in OpenAlex.
- Adaptive responses drive the success of polyploid yellowcresses (Plant diversity · 2022Article
- Examining the utility of DNA barcodes for the identification of tallgrass prairie flora.Applications in plant sciences · 2021Article
- Diet of a rare herbivore based on DNA metabarcoding of feces: Selection, seasonality, and survival.Ecology and evolution · 2020Article
- Fluidigm2PURC: Automated processing and haplotype inference for double-barcoded PCR amplicons.Applications in plant sciences · 2018Article
- A roadmap of phylogenomic methods for studying polyploid plant genera.Applications in plant sciencesArticle
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Authors and funding
7 authors at 5 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
premise of the studyTargeted enrichment strategies for phylogenomic inference are a time- and cost-efficient way to collect DNA sequence data for large numbers of individuals at multiple, independent loci. Automated and reproducible processing of these data is a crucial step for researchers conducting phylogenetic studies. METHODS AND
resultsWe present Fluidigm2PURC, an open source Python utility for processing paired-end Illumina data from double-barcoded PCR amplicons. In combination with the program PURC (Pipeline for Untangling Reticulate Complexes), our scripts process raw FASTQ files for analysis with PURC and use its output to infer haplotypes for diploids, polyploids, and samples with unknown ploidy. We demonstrate the use of the pipeline with an example data set from the genus
conclusionsFluidigm2PURC is freely available for Unix-like operating systems on GitHub (https://github.com/pblischak/fluidigm2purc) and for all operating systems through Docker (https://hub.docker.com/r/pblischak/fluidigm2purc).
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