ArticleFrontiers in genetics2013
Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots.
Article in Frontiers in genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 176 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
176 citing papers in PubMed, 344 citations in OpenAlex.
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- BeeGees: A High-Throughput Protein-Coding DNA Barcode Recovery Pipeline Tailored for Genome Skims of Museum Specimens.Molecular ecology resources · 2026Article
- Reference genome assemblies for the North American bumble bees Bombus flavifrons and Bombus fervidus, two phenotypically polymorphic species from distinct phylogenetic lineages.G3 (Bethesda, Md.) · 2026Article
- Rapidly evolving aphid gall effector proteins exhibit saposin-like folds.bioRxiv : the preprint server for biology · 2026Article
- 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.mSystems · 2026Review
- Improved taxonomic and gene sampling advance the knowledge of deep relationships within Macrodasyida (Gastrotricha).Cladistics : the international journal of the Willi Hennig Society · 2026Article
- Chromosome scale genomes of two invasive Adelges species enable virtual screening for selective adelgicides.G3 (Bethesda, Md.) · 2026Article
- ERGA-CBP chromosome-level genome assembly of the blind scorpionOpen research Europe · 2026Article
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- Genome survey of nutmeg (Frontiers in plant science · 2026Article
- Genomes of the entomopathogenic nematode Steinernema hermaphroditum and its associated bacteria.Genetics · 2025Article
- Symbiotic solutions for colony nutrition: Conserved nitrogen recycling within the bacterial pouch ofProceedings of the National Academy of Sciences of the United States of America · 2025Article
- New reference genome assembly for the declining American Bumble Bee, Bombus pensylvanicus.G3 (Bethesda, Md.) · 2025Article
- Diversity and spread of cytoplasmic incompatibility genes among maternally inherited symbionts.PLoS genetics · 2025Article
- Chromosome scale genomes of two invasive Adelges species enable virtual screening for selective adelgicides.bioRxiv : the preprint server for biology · 2025Article
- Evolutionary Convergence of Nutritional Symbionts in Ticks.Environmental microbiology reports · 2025Article
- Small but Mitey: A Gapless Telomere-to-Telomere Assembly of an Unidentified Mite With a Streamlined Genome.Genome biology and evolution · 2025Article
- A chromosome-level genome assembly of the cabbage aphid Brevicoryne brassicae.Scientific data · 2025Article
116 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Generating the raw data for a de novo genome assembly project for a target eukaryotic species is relatively easy. This democratization of access to large-scale data has allowed many research teams to plan to assemble the genomes of non-model organisms. These new genome targets are very different from the traditional, inbred, laboratory-reared model organisms. They are often small, and cannot be isolated free of their environment - whether ingested food, the surrounding host organism of parasites, or commensal and symbiotic organisms attached to or within the individuals sampled. Preparation of pure DNA originating from a single species can be technically impossible, but assembly of mixed-organism DNA can be difficult, as most genome assemblers perform poorly when faced with multiple genomes in different stoichiometries. This class of problem is common in metagenomic datasets that deliberately try to capture all the genomes present in an environment, but replicon assembly is not often the goal of such programs. Here we present an approach to extracting, from mixed DNA sequence data, subsets that correspond to single species' genomes and thus improving genome assembly. We use both numerical (proportion of GC bases and read coverage) and biological (best-matching sequence in annotated databases) indicators to aid partitioning of draft assembly contigs, and the reads that contribute to those contigs, into distinct bins that can then be subjected to rigorous, optimized assembly, through the use of taxon-annotated GC-coverage plots (TAGC plots). We also present Blobsplorer, a tool that aids exploration and selection of subsets from TAGC-annotated data. Partitioning the data in this way can rescue poorly assembled genomes, and reveal unexpected symbionts and commensals in eukaryotic genome projects. The TAGC plot pipeline script is available from https://github.com/blaxterlab/blobology, and the Blobsplorer tool from https://github.com/mojones/Blobsplorer.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.