ArticleBriefings in bioinformatics2021
A computational toolset for rapid identification of SARS-CoV-2, other viruses and microorganisms from sequencing data.
Article in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 51 citations in OpenAlex.
- META-DIFF: a k-mer-based pipeline that detects differentially abundant sequences in metagenomics whole genome sequencing.Scientific reports · 2026Article
- Deciphering 6-mer Spectra Distribution Rules in Coronavirus Genomes: Application to Comparative Genomic Analysis.International journal of molecular sciences · 2026Article
- Genomic evolution of SARS-CoV-2 delta variants pre- and post-omicron emergence using alignment-free machine learning models.PloS one · 2026Article
- Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus.Genome research · 2025Article
- Diagnostics of viral infections using high-throughput genome sequencing data.Briefings in bioinformatics · 2024Article
- The effects of sequencing strategies on Metagenomic pathogen detection using bronchoalveolar lavage fluid samples.Heliyon · 2024Article
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- Pervasive tandem duplications and convergent evolution shape coral genomes.Genome biology · 2023Article
- A new profiling approach for DNA sequences based on the nucleotides' physicochemical features for accurate analysis of SARS-CoV-2 genomes.BMC genomics · 2023Article
- RabbitTClust: enabling fast clustering analysis of millions of bacteria genomes with MinHash sketches.Genome biology · 2023Article
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- Intrahost SARS-CoV-2 k-mer identification method (iSKIM) for rapid detection of mutations of concern reveals emergence of global mutation patterns.bioRxiv : the preprint server for biology · 2022Article
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- Molecular Characteristics and Incidence of Apple Rubbery Wood Virus 2 and Citrus Virus A Infecting Pear Trees in China.Viruses · 2022Article
- Review
- VirStrain: a strain identification tool for RNA viruses.Genome biology · 2022Article
- Measuring the Invisible: The Sequences Causal of Genome Size Differences in Eyebrights (Frontiers in plant science · 2022Article
- Rapid screening and identification of viral pathogens in metagenomic data.BMC medical genomics · 2021Article
- COVID-19-associated inhibition of energy accumulation pathways in human semen samples.F&S science · 2021Observational
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this paper, we present a toolset and related resources for rapid identification of viruses and microorganisms from short-read or long-read sequencing data. We present fastv as an ultra-fast tool to detect microbial sequences present in sequencing data, identify target microorganisms and visualize coverage of microbial genomes. This tool is based on the k-mer mapping and extension method. K-mer sets are generated by UniqueKMER, another tool provided in this toolset. UniqueKMER can generate complete sets of unique k-mers for each genome within a large set of viral or microbial genomes. For convenience, unique k-mers for microorganisms and common viruses that afflict humans have been generated and are provided with the tools. As a lightweight tool, fastv accepts FASTQ data as input and directly outputs the results in both HTML and JSON formats. Prior to the k-mer analysis, fastv automatically performs adapter trimming, quality pruning, base correction and other preprocessing to ensure the accuracy of k-mer analysis. Specifically, fastv provides built-in support for rapid severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) identification and typing. Experimental results showed that fastv achieved 100% sensitivity and 100% specificity for detecting SARS-CoV-2 from sequencing data; and can distinguish SARS-CoV-2 from SARS, Middle East respiratory syndrome and other coronaviruses. This toolset is available at: https://github.com/OpenGene/fastv.
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