ArticleBioinformatics (Oxford, England)2012
Reference-independent comparative metagenomics using cross-assembly: crAss.
Article in Bioinformatics (Oxford, England), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities.Science advances · 2026Article
- Solving genomic puzzles: computational methods for metagenomic binning.Briefings in bioinformatics · 2024Review
- Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee.Archives of virology · 2023Article
- PathoLive-Real-Time Pathogen Identification from Metagenomic Illumina Datasets.Life (Basel, Switzerland) · 2022Article
- Music of metagenomics-a review of its applications, analysis pipeline, and associated tools.Functional & integrative genomics · 2022Review
- Unraveling the viral dark matter through viral metagenomics.Frontiers in immunology · 2022Review
- Metagenome SNP calling via read-colored de Bruijn graphs.Bioinformatics (Oxford, England) · 2021Article
- Article
- Shining Light on Human Gut Bacteriophages.Frontiers in cellular and infection microbiology · 2020Review
- Cyanobacterial biodiversity of semiarid public drinking water supply reservoirs assessed via next-generation DNA sequencing technology.Journal of microbiology (Seoul, Korea) · 2019Article
- Recentrifuge: Robust comparative analysis and contamination removal for metagenomics.PLoS computational biology · 2019Article
- Gut Bacteriophage: Current Understanding and Challenges.Frontiers in endocrinology · 2019Review
- On the Role of Bioinformatics and Data Science in Industrial Microbiome Applications.Frontiers in genetics · 2019Article
- Novel phages of healthy skin metaviromes from South Africa.Scientific reports · 2018Article
- Article
- Metagenomics of Coral Reefs Under Phase Shift and High Hydrodynamics.Frontiers in microbiology · 2018Article
- The Human Virome Protein Cluster Database (HVPC): A Human Viral Metagenomic Database for Diversity and Function Annotation.Frontiers in microbiology · 2018Article
- Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes.BMC genomics · 2017Article
- Environmental drivers of viral community composition in Antarctic soils identified by viromics.Microbiome · 2017Article
- Review
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7 authors.
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No grant is acknowledged in the PubMed record.
Abstract
motivationMetagenomes are often characterized by high levels of unknown sequences. Reads derived from known microorganisms can easily be identified and analyzed using fast homology search algorithms and a suitable reference database, but the unknown sequences are often ignored in further analyses, biasing conclusions. Nevertheless, it is possible to use more data in a comparative metagenomic analysis by creating a cross-assembly of all reads, i.e. a single assembly of reads from different samples. Comparative metagenomics studies the interrelationships between metagenomes from different samples. Using an assembly algorithm is a fast and intuitive way to link (partially) homologous reads without requiring a database of reference sequences.
resultsHere, we introduce crAss, a novel bioinformatic tool that enables fast simple analysis of cross-assembly files, yielding distances between all metagenomic sample pairs and an insightful image displaying the similarities.
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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.