Biology subjects

Prosser, S. W.

Publications and source records attributed to Prosser, S. W..

7 recordsLinked to original sources

bioRxiv2026

The Barcode Inference Pipeline (BIP): From Sequencer Output to DNA Barcodes

DNA barcoding involves the recovery of a DNA sequence for a target gene region from its source specimen. This process gains complexity when multiple sequences are recovered from a specimen, as is often the case when data are generated by high-throughput sequencers. This diversity can reflect both methodological artifacts (e.g., chimeras, PCR errors, sequencing errors, tag jumps) and real template diversity in the DNA extract (e.g., contamination, endosymbionts, NUMTs, parasites). To support analysis of the sequence data from three million specimens annually, the Centre for Biodiversity Genomics (CBG) has developed BIP, the Barcode Inference Pipeline. Compatible with all sequencing platforms, BIP processes .fastq files and returns both target DNA barcodes and non-target sequences. To generate results, BIP implements quality and size filtration, demultiplexing, primer trimming, chimera scanning, sequence error correction, OTU delineation, and sequence identification. When analysis targets the cytochrome c oxidase 1 (COI) barcode region, BIP also assigns each OTU to a known BIN or identifies its nearest neighbour BIN. As final output, BIP returns summary files ready for upload to BOLD or for other downstream analyses. They include a taxonomic assignment for each OTU, generated by comparison with a DNA barcode reference library. We describe BIPs flexibility and structure, then demonstrate its functionality by analyzing COI sequence data from 100K specimens. Because of its capacity to disentangle target and non-target sequences, BIP outperforms an alternative software package, ONTbarcoder, in several important ways. To ease access, installation, and functionality, BIP is provided as a Docker container (github.com/cbg-innov/BIP).

bioinformatics↗

bioRxiv2026

The Metabarcoding Analysis Pipeline (MAP): Simple, accurate, and flexible metabarcoding

Current metabarcoding pipelines are inflexible with respect to study design and are poorly suited to long-read sequence data. To address these limitations, we developed MAP, the Metabarcoding Analysis Pipeline, which is a sequence-to-answer workflow supporting the analysis of amplicons from highly multiplexed and replicated study designs. Although MAP can analyze amplicons of any length from any genetic marker, it includes several features tailored to long-read COI metabarcoding. MAP installs from a Docker container and requires only sequence data, a parameters file, and a reference library. It produces intuitive reports, enabling users to evaluate their data immediately after analysis. We validate MAP by showing that it generates biodiversity estimates that correspond closely to a ground-truth dataset of single-specimen DNA barcode data and by demonstrating that it outperforms alternative platforms for COI metabarcoding. MAP is free, open-source, and available from: https://github.com/cbg-innov/MAP.

bioinformatics↗

bioRxiv2026

Performance Test of the QNome Nanopore Sequencer

Nanopore sequencers have the potential to liberate DNA sequencing from centralized core facilities to distributed analytical nodes. Until now, Oxford Nanopore Technologies (ONT) has been the sole manufacturer of a portable nanopore sequencer, but analogous platforms are in production. Nanopore sequencers from Qitan Technology (QT) are widely used in China but have been unavailable outside that nation and lack independent performance testing. Enabled by early access to QTs least expensive sequencer and flow cell, the QNome-3841 and QCell-384, we tested whether they could generate accurate DNA barcodes cost-effectively. In several tests involving amplicon pools from 95 to 9,120 specimens, QT recovered valid DNA barcodes from nearly as many specimens (98%) as ONT. QT sequences had slightly lower fidelity than their ONT counterparts and QT frequently failed to resolve the correct length of G/C homopolymers. However, barcode sequences from the two platforms were nearly indistinguishable after bioinformatic treatment. QTs wash kit performed well, enabling a QCell to sequence eight amplicon pools with zero carryover between runs and minimal degradation of the flow cell. Its ultra-fast protocol allowed library preparation in a single step that could be completed in 15 minutes, but this came at the cost of lower quality data. Once widely available, QT devices will be well-suited for supporting DNA barcode analysis.

genomics↗

bioRxiv2021

Message in a Bottle, Metabarcoding Enables Biodiversity Comparisons Across Ecoregions

BackgroundTraditional biomonitoring approaches have delivered a basic understanding of biodiversity, but they cannot support the large-scale assessments required to manage and protect entire ecosystems. This study employed DNA metabarcoding to assess spatial and temporal variation in species richness and diversity in arthropod communities from 52 protected areas spanning three Canadian ecoregions. ResultsThis study revealed the presence of 26,263 arthropod species in the three ecoregions and indicated that at least another 3,000-5,000 await detection. Results further demonstrate that communities are more similar within than between ecoregions, even after controlling for geographical distance. Overall -diversity declined from east to west, reflecting a gradient in habitat disturbance. Shifts in species composition were high at every site with turnover greater than nestedness, suggesting the presence of many transient species. ConclusionsDifferences in species composition among their arthropod communities confirm that ecoregions are a useful synoptic for biogeographic patterns and for structuring conservation efforts. The present results also demonstrate that metabarcoding enables large-scale monitoring of shifts in species composition, making it possible to move beyond the biomass measurements that have been the key metric employed in prior efforts to track change in arthropod communities.

ecology↗

bioRxiv2020

Massive Multiplexing Can Deliver a $1 Test for COVID-19

The severe acute respiratory syndrome virus, SARS-CoV-2 (hereafter COVID-19), rapidly achieved global pandemic status, provoking large-scale screening programs in many nations. Their activation makes it imperative to identify methods that can deliver a diagnostic result at low cost. This paper describes an approach which employs sequence variation in the gene coding for its envelope protein as the basis for a scalable, inexpensive test for COVID-19. It achieves this by coupling a simple RNA extraction protocol with low-volume RT-PCR, followed by E-Gel screening and sequencing on high-throughput platforms to analyze 10,000 samples in a run. Slight modifications to the protocol could support screening programs for other known viruses and for viral discovery. Just as the $1,000 genome is transforming medicine, a $1 diagnostic test for viral and bacterial pathogens would represent a major advance for public health.

genomics↗

bioRxiv2018

Revealing the Complexities of Metabarcoding with a Diverse Arthropod Mock Community

DNA metabarcoding is an attractive approach for monitoring biodiversity. However, it is subject to biases that often impede detection of all species in a sample. In particular, the proportion of sequences recovered from each species depends on its biomass, mitome copy number, and primer set employed for PCR. To examine these variables, we constructed a mock community of terrestrial arthropods comprised of 374 BINs, a species proxy. We used this community to examine how species recovery was impacted when amplicon pools were constructed in four ways. The first two protocols involved the construction of bulk DNA extracts from different body partitions (Bulk Abdomen, Bulk Leg). The other protocols involved the production of DNA extracts from single legs which were then merged prior to PCR (Composite Leg) or PCR-amplified separately (Single Leg) and then pooled. The amplicon generated by these four treatments were then sequenced on three platforms (Illumina MiSeq, Ion Torrent PGM and Ion Torrent S5). The choice of sequencing platform did not substantially influence species recovery, other variables did. As expected, the best recovery was obtained from the Single Leg treatment, but the Bulk Abdomen produced a more uniform read abundance than the Bulk Leg or Composite Leg samples. Primer choice also influenced species recovery. Our results reveal how variation in protocols can have substantive impacts on perceived diversity unless sequencing coverage is sufficient to reach an asymptote. Although metabarcoding is a powerful approach, further optimization of analytical protocols is crucial to obtain reproducible results and increase its cost-effectiveness.

ecology↗

bioRxiv2017

A Sequel to Sanger: Amplicon Sequencing That Scales

Although high-throughput sequencers (HTS) have largely displaced their Sanger counterparts, the short read lengths and high error rates of most platforms constrain their utility for amplicon sequencing. The present study tests the capacity of single molecule, real-time (SMRT) sequencing implemented on the SEQUEL platform to overcome these limitations, employing 658 bp amplicons of the mitochondrial cytochrome c oxidase I gene as a model system. By examining templates from more than 5,000 species and 20,000 specimens, the performance of SMRT sequencing was tested with amplicons showing wide variation in GC composition and varied sequence attributes. SMRT and Sanger sequences were very similar, but SMRT sequencing provided more complete coverage, especially for amplicons with homopolymer tracts. Because it can characterize amplicon pools from 10,000 DNA extracts in a single run, the SEQUEL reduces costs 40-fold from Sanger analysis. Reflecting the capacity of each instrument to recover sequences from more than five million DNA extracts a year, this platform facilitates massive amplicon characterization.

molecular biology↗