ArticleMicrobiome2015
Xander: employing a novel method for efficient gene-targeted metagenomic assembly.
Article in Microbiome, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
- Metagenomic Insights into the Degradation of Resistant Starch by Human Gut Microbiota.Applied and environmental microbiology · 2018Trial
- Enhancement of genetic potential for soil carbon and nitrogen cycling by organic fertilizer substitution improves the ecological environment for licorice cultivation.Frontiers in microbiology · 2026Article
- Targeted assembly recovers high ammonia monooxygenase diversity in mudflat intertides.mSystems · 2025Article
- Impact of Biochar Addition on Biofloc Nitrifying Bacteria and Inorganic Nitrogen Dynamics in an Intensive Aquaculture System of Shrimp.Microorganisms · 2024Article
- Soil Microbial Community Involved in Nitrogen Cycling in Rice Fields Treated with Antiozonant under Ambient Ozone.Applied and environmental microbiology · 2023Article
- IntegratedNAR genomics and bioinformatics · 2023Article
- Article
- Strategies and tools in illumina and nanopore-integrated metagenomic analysis of microbiome data.iMeta · 2023Review
- Review
- Music of metagenomics-a review of its applications, analysis pipeline, and associated tools.Functional & integrative genomics · 2022Review
- MCRL: using a reference library to compress a metagenome into a non-redundant list of sequences, considering viruses as a case study.Bioinformatics (Oxford, England) · 2022Article
- Butyrate Production Pathway Abundances Are Similar in Human and Nonhuman Primate Gut Microbiomes.Molecular biology and evolution · 2022Article
- Aryl Hydrocarbon Receptor (AhR) Activation by 2,3,7,8-Tetrachlorodibenzo-International journal of molecular sciences · 2021Article
- Genome-resolved metagenomics using environmental and clinical samples.Briefings in bioinformatics · 2021Review
- Molecular Communications in Viral Infections Research: Modeling, Experimental Data, and Future Directions.IEEE transactions on molecular, biological, and multi-scale communications · 2021Article
- ORFograph: search for novel insecticidal protein genes in genomic and metagenomic assembly graphs.Microbiome · 2021Article
- Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems.Microbiome · 2021Article
- Spinal Cord Injury Changes the Structure and Functional Potential of Gut Bacterial and Viral Communities.mSystems · 2021Article
- ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data.BMC bioinformatics · 2021Article
- DRAGoM: Classification and Quantification of Noncoding RNA in Metagenomic Data.Frontiers in genetics · 2021Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
backgroundMetagenomics can provide important insight into microbial communities. However, assembling metagenomic datasets has proven to be computationally challenging. Current methods often assemble only fragmented partial genes.
resultsWe present a novel method for targeting assembly of specific protein-coding genes. This method combines a de Bruijn graph, as used in standard assembly approaches, and a protein profile hidden Markov model (HMM) for the gene of interest, as used in standard annotation approaches. These are used to create a novel combined weighted assembly graph. Xander performs both assembly and annotation concomitantly using information incorporated in this graph. We demonstrate the utility of this approach by assembling contigs for one phylogenetic marker gene and for two functional marker genes, first on Human Microbiome Project (HMP)-defined community Illumina data and then on 21 rhizosphere soil metagenomic datasets from three different crops totaling over 800 Gbp of unassembled data. We compared our method to a recently published bulk metagenome assembly method and a recently published gene-targeted assembler and found our method produced more, longer, and higher quality gene sequences.
conclusionXander combines gene assignment with the rapid assembly of full-length or near full-length functional genes from metagenomic data without requiring bulk assembly or post-processing to find genes of interest. HMMs used for assembly can be tailored to the targeted genes, allowing flexibility to improve annotation over generic annotation pipelines. This method is implemented as open source software and is available at https://github.com/rdpstaff/Xander_assembler.
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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.