ArticleBMC bioinformatics2018
PIPEBAR and OverlapPER: tools for a fast and accurate DNA barcoding analysis and paired-end assembly.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
3 citing papers in PubMed, 17 citations in OpenAlex.
- DNA-Barcoding for Cultivar Identification and Intraspecific Diversity Analysis of Agricultural Crops.International journal of molecular sciences · 2025Review
- Unraveling the plant diversity of the AmazonianEcology and evolution · 2021Article
- BigFiRSt: A Software Program Using Big Data Technique for Mining Simple Sequence Repeats From Large-Scale Sequencing Data.Frontiers in big data · 2021Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundTaxonomic identification of plants and insects is a hard process that demands expert taxonomists and time, and it's often difficult to distinguish on morphology only. DNA barcodes allow a rapid species discovery and identification and have been widely used for taxonomic identification by targeting known gene regions that permit to discriminate these species. DNA barcode sequence analysis is usually carried out with processes and tools that still demand a high interaction with the user or researcher. To reduce at most such interaction, we proposed PIPEBAR, a pipeline for DNA chromatograms analysis of Sanger platform sequencing, ensuring high quality consensus sequences along with efficient running time. We also proposed a paired-end reads assembly tool, OverlapPER, which is used in sequence or independently of PIPEBAR.
resultsPIPEBAR is a command line tool to automatize the processing of large number of trace files. It is accurate as the proprietary Geneious tool and faster than most popular software for barcoding analysis. It is 7 times faster than Geneious and 14 times faster than SeqTrace for processing hundreds of barcoding sequences. OverlapPER is a novel tool for overlapping paired-end reads accurately that accepts both substitution and indel errors and returns both overlapped and non-overlapped regions between a pair of reads. OverlapPER obtained the best results compared to currently used tools when merging 1,000,000 simulated paired-end reads.
conclusionsPIPEBAR and OverlapPER run on most operating systems and are freely available, along with supporting code and documentation, at https://sourceforge.net/projects/PIPEBAR / and https://sourceforge.net/projects/overlapper-reads /.
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