ArticleGenome research2018
taxMaps: comprehensive and highly accurate taxonomic classification of short-read data in reasonable time.
Article in Genome research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Report of the fourth conference on next-generation sequencing (NGS) for adventitious virus detection in biologics for humans and animals: Validation and implementation of NGS.Biologicals : journal of the International Association of Biological Standardization · 2025Article
- Application and Comparison of Machine Learning and Database-Based Methods in Taxonomic Classification of High-Throughput Sequencing Data.Genome biology and evolution · 2024Article
- Matchtigs: minimum plain text representation of k-mer sets.Genome biology · 2023Article
- Exercise and microbiome: From big data to therapy.Computational and structural biotechnology journal · 2023Review
- A translational genomics approach identifies IL10RB as the top candidate gene target for COVID-19 susceptibility.NPJ genomic medicine · 2022Article
- Nanopore sequencing of a monkeypox virus strain isolated from a pustular lesion in the Central African Republic.Scientific reports · 2022Article
- Generation and application of pseudo-long reads for metagenome assembly.GigaScience · 2022Article
- Orchestrating an Optimized Next-Generation Sequencing-Based Cloud Workflow for Robust Viral Identification during Pandemics.Biology · 2021Article
- IL10RB as a key regulator of COVID-19 host susceptibility and severity.medRxiv : the preprint server for health sciences · 2021Article
- Review
- Simplitigs as an efficient and scalable representation of de Bruijn graphs.Genome biology · 2021Article
- IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring.GigaScience · 2020Article
- BITS2019: the sixteenth annual meeting of the Italian society of bioinformatics.BMC bioinformatics · 2020Article
- Metagenomic analysis through the extended Burrows-Wheeler transform.BMC bioinformatics · 2020Article
- Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses.Microbial genomics · 2020Review
- The genome of a subterrestrial nematode reveals adaptations to heat.Nature communications · 2019Article
- Review
- MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples.BMC genomics · 2019Article
Corrections and comments
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
High-throughput sequencing is a revolutionary technology for the analysis of metagenomic samples. However, querying large volumes of reads against comprehensive DNA/RNA databases in a sensitive manner can be compute-intensive. Here, we present taxMaps, a highly efficient, sensitive, and fully scalable taxonomic classification tool. Using a combination of simulated and real metagenomics data sets, we demonstrate that taxMaps is more sensitive and more precise than widely used taxonomic classifiers and is capable of delivering classification accuracy comparable to that of BLASTN, but at up to three orders of magnitude less computational cost.
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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.