PIPEBAR and OverlapPER: tools for a fast and accurate DNA barcoding analysis and paired-end assembly

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/.Electronic supplementary materialThe online version of this article (10.1186/s12859-018-2307-y) contains supplementary material, which is available to authorized users.

BIOCHEMICAL CHARACTERIZATION OF Ferula rutbaensis MEDICINAL PLANT IN IRAQI WESTERN DESERT

“…Taxonomic identification of plant species is a very delicate and time-consuming process. It requires competent experts who are able to distinguish between even closely related species based on their complex phenotypic characteristics (Oliveira et al, 2018). Unfortunately, like any other technique that relies on human skill, it may reflect in unreliable results.…”

Molecular evidence for Myripristisjacobus and Scarustaeniopterus new to Bay of Bengal: Sporadic appearance or preliminary colonization?

“…Continuous sequence reads of high‐quality bases (Quality value (QV)>20) were considered for further analysis. Both the chromatograms (forward and reverse) were analyzed, and the correct barcode sequences were generated with the program PIPEBAR and OverlapPER (Oliveira et al., 2018). The generated sequences were further aligned in MAFFT v7.428 (Katoh & Standley, 2013), translated, and checked for the presence of elevated nonsynonymous substitutions or frameshifts of codons in MEGA X (Kumar et al., 2018) because these signatures can indicate the presence of nuclear mtDNA copies.…”

DNA-based approaches for dairy products authentication: A review and perspectives

“…DNA barcodes generated through the traditional Sanger sequencing can be analysed (quality check, filtering, reads overlapping and format conversion) using open source tools such as SPIDER (Brown et al, 2012), ClinQC (Pandey, Pabinger, Kriegner, & Weinhäusel, 2016) and SeqTrace (Stucky, 2012). Recently, an automated pipeline for Sanger sequence DNA barcode analysis, PIPEBAR was developed by Oliveira et al (Oliveira, Nunes, de Lima, Oliveira, & Alves, 2018).…”