ArticleBioinformatics (Oxford, England)2019
GenCoF: a graphical user interface to rapidly remove human genome contaminants from metagenomic datasets.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Application of Metagenomic Next-Generation Sequencing inFrontiers in medicine · 2022Pooled it
- Article
- Protocol for the assessment of the impact of mycotoxins and glyphosate residues on the gut microbiome and resistome of European fallow deer.STAR protocols · 2026Article
- Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives.Briefings in bioinformatics · 2025Review
- Monitoring Changes in the Antimicrobial-Resistance Gene Set (ARG) of Raw Milk and Dairy Products in a Cattle Farm, from Production to Consumption.Veterinary sciences · 2024Article
- Modeling the limits of detection for antimicrobial resistance genes in agri-food samples: a comparative analysis of bioinformatics tools.BMC microbiology · 2024Article
- HoCoRT: host contamination removal tool.BMC bioinformatics · 2023Article
- Background Filtering of Clinical Metagenomic Sequencing with a Library Concentration-Normalized Model.Microbiology spectrum · 2022Article
- MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences.Frontiers in genetics · 2022Article
- Natural diversity of the honey bee (Apis mellifera) gut bacteriome in various climatic and seasonal states.PloS one · 2022Article
- Genome-resolved metagenomics using environmental and clinical samples.Briefings in bioinformatics · 2021Review
- ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach.PLoS computational biology · 2021Article
- Metagenomic insights of the infant microbiome community structure and function across multiple sites in the United States.Scientific reports · 2021Article
- High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings.Small methods · 2021Review
- Impact of ProbioticFrontiers in pediatrics · 2021Article
- Evaluation of methods for detecting human reads in microbial sequencing datasets.Microbial genomics · 2020Article
- Microbial community analysis using high-throughput sequencing technology: a beginner's guide for microbiologists.Journal of microbiology (Seoul, Korea) · 2020Article
- Early-life gut microbiome modulation reduces the abundance of antibiotic-resistant bacteria.Antimicrobial resistance and infection control · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryThe removal of human genomic reads from shotgun metagenomic sequencing is a critical step in protecting subject privacy. Freely available tools addressing this issue require advanced programing knowledge or are limited by analytical time and data load due to their server-based nature. Here, we compared the most cited tools for host-DNA removal using synthetic and real metagenomic datasets. Then, we integrated the most efficient pipeline in a graphical user interface to make these tools available without command line use. This interface, GenCoF, rapidly removes human genome contaminants from metagenomic datasets. Additionally, the tool offers quality-filtering, data reduction and interactive modification of any parameter in order to customize the analysis. GenCoF offers both quality and host-associated filtering in a non-commercial, freely available tool in a local, interactive and easy-to-use interface. AVAILABILITY AND IMPLEMENTATION: GenCoF is freely available (under a GPL license) for Mac OS and Linux at https://github.com/MattCzajkowski/GenCoF. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.