ArticleNucleic acids research2013
Crass: identification and reconstruction of CRISPR from unassembled metagenomic data.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 papers.
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Who cites it
97 citing papers in PubMed.
- Virus-mediated prokaryotic community adaptation dynamics under thermal stress in municipal organic solid waste microbiomes.Communications biology · 2026Article
- Quantitative stable isotope probing (qSIP)-informed metagenomics identifies viruses infecting chemoautotrophs.Nature communications · 2026Article
- Article
- Diversity, transfer potential, and transcriptional activity of virus-carried antibiotic resistance genes in global estuaries.iMetaOmics · 2026Article
- Host-linked virome assembly and turnover predict bacterial community structure in wastewater treatment systems.The ISME journal · 2026Article
- Deep-sea viral diversity and their role in host metabolism of complex organic matter.Nature communications · 2025Article
- CRISPR-GATE: a one-stop repository and guide to computational resources for genome editing experimentation.Briefings in bioinformatics · 2025Review
- Integrating metagenomics and cultivation unveils oral phage diversity and potential impact on hosts.NPJ biofilms and microbiomes · 2025Article
- Evolutionary trends inmSystems · 2025Article
- CRISPR-Cas9 and Its Bioinformatics Tools: A Systematic Review.Current issues in molecular biology · 2025Review
- CRISPR-Cas spacer acquisition is a rare event in human gut microbiome.Cell genomics · 2025Article
- Multiple roles of DNA methylation in sea-ice bacterial communities and associated viruses.The ISME journal · 2025Article
- Long-term metagenomic insights into the roles of antiviral defense systems in stabilizing activated sludge bacterial communities.The ISME journal · 2025Article
- Metagenomic CRISPR Array Analysis Tool: a novel graph-based approach to finding CRISPR arrays in metagenomic datasets.microLife · 2025Article
- Correlation between the gut microbiome and neurodegenerative diseases: a review of metagenomics evidence.Neural regeneration research · 2024Review
- Trade-offs between receptor modification and fitness drive host-bacteriophage co-evolution leading to phage extinction or co-existence.The ISME journal · 2024Article
- High niche specificity and host genetic diversity of groundwater viruses.The ISME journal · 2024Article
- Host-specific viral predation network on coral reefs.The ISME journal · 2024Article
- Freshwater Viral Metagenome Analyses Targeting dsDNA Viruses.Methods in molecular biology (Clifton, N.J.) · 2024Article
- 3Bs of CRISPR-Cas mediated genome editing in plants: exploring the basics, bioinformatics and biosafety landscape.Physiology and molecular biology of plants : an international journal of functional plant biology · 2023Review
37 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) constitute a bacterial and archaeal adaptive immune system that protect against bacteriophage (phage). Analysis of CRISPR loci reveals the history of phage infections and provides a direct link between phage and their hosts. All current tools for CRISPR identification have been developed to analyse completed genomes and are not well suited to the analysis of metagenomic data sets, where CRISPR loci are difficult to assemble owing to their repetitive structure and population heterogeneity. Here, we introduce a new algorithm, Crass, which is designed to identify and reconstruct CRISPR loci from raw metagenomic data without the need for assembly or prior knowledge of CRISPR in the data set. CRISPR in assembled data are often fragmented across many contigs/scaffolds and do not fully represent the population heterogeneity of CRISPR loci. Crass identified substantially more CRISPR in metagenomes previously analysed using assembly-based approaches. Using Crass, we were able to detect CRISPR that contained spacers with sequence homology to phage in the system, which would not have been identified using other approaches. The increased sensitivity, specificity and speed of Crass will facilitate comprehensive analysis of CRISPRs in metagenomic data sets, increasing our understanding of phage-host interactions and co-evolution within microbial communities.
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