BBMerge – Accurate paired shotgun read merging via overlap

Bushnell, Brian; Rood, Jonathan; Singer, Esther

doi:10.1371/journal.pone.0185056

Cited by 1,065 publications

(898 citation statements)

References 21 publications

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“…BBMerge (v.37. 36) [27] was used to merge overlapping pairs of reads using default parameters. Forward reads showed very high quality scores; therefore, those that did not merge were extracted from the bbmerge unmerged output file (https://github.com/pjtorres/xtract_forward) as to not discard useful data.…”

Section: Methodsmentioning

confidence: 99%

Discovery of a Novel Periodontal Disease-Associated Bacterium

et al. 2018

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One of the world's most common infectious disease, periodontitis (PD), derives from largely uncharacterized communities of oral bacteria growing as biofilms (a.k.a. plaque) on teeth and gum surfaces in periodontal pockets. Bacteria associated with periodontal disease trigger inflammatory responses in immune cells, which in later stages of the disease cause loss of both soft and hard tissue structures supporting teeth. Thus far, only a handful of bacteria have been characterized as infectious agents of PD. Although deep sequencing technologies, such as whole community shotgun sequencing have the potential to capture a detailed picture of highly complex bacterial communities in any given environment, we still lack major reference genomes for the oral microbiome associated with PD and other diseases. In recent work, by using a combination of supervised machine learning and genome assembly, we identified a genome from a novel member of the Bacteroidetes phylum in periodontal samples. Here, by applying a comparative metagenomics read-classification approach, including 272 metagenomes from various human body sites, and our previously assembled draft genome of the uncultivated Candidatus Bacteroides periocalifornicus (CBP) bacterium, we show CBP's ubiquitous distribution in dental plaque, as well as its strong association with the well-known pathogenic "red complex" that resides in deep periodontal pockets.

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Section: Methodsmentioning

confidence: 99%

Discovery of a Novel Periodontal Disease-Associated Bacterium

et al. 2018

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“…Prior to assembly, the "cleaned-reads" were further processed to decrease computational load and increase accuracy. We merged paired-end reads using BBMerge (Bushnell et al 2017) from BBTools. BBMerge also fills in missing gaps between non-overlapping paired-end reads by assembling missing data from the other paired-end reads using the "Tadpole" program.…”

Section: Reduced-ranoidea Marker Selectionmentioning

confidence: 99%

FrogCap: A modular sequence capture probe set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales

Hutter

Cobb

Portik

et al. 2019

Preprint

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Despite the increasing use of high-throughput sequencing in phylogenetics, many phylogenetic relationships remain difficult to resolve because of conflict between gene trees and species trees. Selection of different types of markers (i.e. protein-coding exons, non-coding introns, ultraconserved elements) is becoming important to alleviate these phylogenomic challenges. For evolutionary studies in frogs, we introduce the new publicly available FrogCap suite of genomic resources, which is a large and flexible collection of probes corresponding to ~15,000 markers that unifies previous frog sequencing work. FrogCap is designed to be modular, such that subsets of markers can be selected based on the phylogenetic scale of the intended study. FrogCap uses a variety of molecular marker types that include newly obtained exons and introns, previously sequenced UCEs, and Sanger-sequencing markers, which span a range of alignment lengths (100-12,000 base pairs). We tested three probe sets from FrogCap using 105 samples across five phylogenetic scales, comparing probes designed using a consensus-or genome-based approach. We also tested the effects of using different bait kit sizes on depth of coverage and missing data. We found that larger bait kits did not result in lowered depth of coverage or increased missing data. We also found that sensitivity, specificity, and missing data are not related to genetic distance in the consensus-based probe design, suggesting that this approach has greater success and overcomes a major hurdle in probe design. We observed sequence capture success (in terms of missing data, quantity of sequence data, recovered marker length, and number of informative sites) and compared them at all phylogenetic scales. The incorporation of different molecular marker types allowed recovery of the variation required for resolving difficult phylogenetic relationships and for performing population genetic studies. Altogether, FrogCap is a valuable and adaptable resource for performing high-throughput sequencing projects across variable timescales.

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“…Read length filters of a minimum of 50 bp and a maximum of 95 bp were applied to reads produced from the NovaSeq 6000, as a much larger percentage of the reads from those libraries were <20 bp after adapter trimming. For paired-end data, BBMerge from the BBTools software package was used to merge R1 and R2 read pairs into a consensus sequence (Bushnell et al 2017).…”

Section: Sequencing and Read Processingmentioning

confidence: 99%

Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification

Warren

Salinas‐Giegé

Hummel

et al. 2019

Preprint

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Differences in tRNA expression have been implicated in a remarkable number of biological processes.There is growing evidence that tRNA genes can play dramatically different roles depending on both expression and post-transcriptional modification, yet sequencing tRNAs to measure abundance and detect modifications remains challenging. Their secondary structure and extensive post-transcriptional modifications interfere with RNA-seq library preparation methods and have limited the utility of highthroughput sequencing technologies. Here, we combine two modifications to standard RNA-seq methods by treating with the demethylating enzyme AlkB and ligating with tRNA-specific adapters in order to sequence tRNAs from four species of flowering plants, a group that has been shown to have some of the most extensive rates of post-transcriptional tRNA modifications. This protocol has the advantage of detecting full-length tRNAs and sequence variants that can be used to infer many post-transcriptional modifications. We used the resulting data to produce a modification index of almost all unique reference tRNAs in Arabidopsis thaliana, which exhibited many anciently conserved similarities with humans but also positions that appear to be "hot spots" for modifications in angiosperm tRNAs. We also found evidence based on northern blot analysis and droplet digital PCR that, even after demethylation treatment, tRNA-seq can produce highly biased estimates of absolute expression levels most likely due to biased reverse transcription. Nevertheless, the generation of full-length tRNA sequences with modification data is still promising for assessing differences in relative tRNA expression across treatments, tissues or subcellular fractions and help elucidate the functional roles of tRNA modifications.

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BBMerge – Accurate paired shotgun read merging via overlap

Cited by 1,065 publications

References 21 publications

Discovery of a Novel Periodontal Disease-Associated Bacterium

Discovery of a Novel Periodontal Disease-Associated Bacterium

FrogCap: A modular sequence capture probe set for phylogenomics and population genetics for all frogs, assessed across multiple phylogenetic scales

Combining tRNA sequencing methods to characterize plant tRNA expression and post-transcriptional modification

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