The problem of supervised DNA sequence classification arises in several fields of computational molecular biology. Although this problem has been extensively studied, it is still computationally challenging due to size of the datasets that modern sequencing technologies can produce. We introduce CLARK a novel approach to classify metagenomic reads at the species or genus level with high accuracy and high speed. Extensive experimental results on various metagenomic samples show that the classification accuracy of CLARK is better or comparable to the best state-of-the-art tools and it is significantly faster than any of its competitors. In its fastest single-threaded mode CLARK classifies, with high accuracy, about 32 million metagenomic short reads per minute. CLARK can also classify BAC clones or transcripts to chromosome arms and centromeric regions. CLARK is a versatile, fast and accurate sequence classification method, especially useful for metagenomics and genomics applications. It is freely available at http://clark.cs.ucr.edu/ .
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StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees
rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison
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CLAME: a new alignment-based binning algorithm allows the genomic description of a novel Xanthomonadaceae from the Colombian Andes
Serotonin Transporter Deficiency is Associated with Dysbiosis and Changes in Metabolic Function of the Mouse Intestinal Microbiome.
Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism
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The impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters
SEPATH: benchmarking the search for pathogens in human tissue whole genome sequence data leads to template pipelines
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TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganisms
Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa's Environmental Regimes
Analysis of sequencing strategies and tools for taxonomic annotation: Defining standards for progressive metagenomics
Identification of Major Rhizobacterial Taxa Affected by a Glyphosate-Tolerant Soybean Line via Shotgun Metagenomic Approach
Comparison of Database Search Methods for the Detection of Legionella pneumophila in Water Samples Using Metagenomic Analysis
Identification and quantitation of clinically relevant microbes in patient samples: Comparison of three k-mer based classifiers for speed, accuracy, and sensitivity
MiCoP: microbial community profiling method for detecting viral and fungal organisms in metagenomic samples
Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools
Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method
Method for the Identification of Plant DNA in Food Using Alignment-Free Analysis of Sequencing Reads: A Case Study on Lupin
Mismatch-tolerant, alignment-free sequence classification using multiple spaced seeds and multiindex Bloom filters
k-SLAM: accurate and ultra-fast taxonomic classification and gene identification for large metagenomic data sets
Considerations for Optimization of High-Throughput Sequencing Bioinformatics Pipelines for Virus Detection
ConFindr: rapid detection of intraspecies and cross-species contamination in bacterial whole-genome sequence data
Quantitative Framework for Model Evaluation in Microbiology Research Using Pseudomonas aeruginosa and Cystic Fibrosis Infection as a Test Case
A Comparison of Two DNA Metagenomic Bioinformatic Pipelines While Evaluating the Microbial Diversity in Feces of Tanzanian Small Holder Dairy Cattle
Unique k -mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling
Testing the advantages and disadvantages of short- and long- read eukaryotic metagenomics using simulated reads
CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data.
Comparison of methods for library construction and short read annotation of shellfish viral metagenomes
Complex Evolutionary History of Translation Elongation Factor 2 and Diphthamide Biosynthesis in Archaea and Parabasalids
Toward an Alignment-Free Method for Feature Extraction and Accurate Classification of Viral Sequences
A novel data structure to support ultra-fast taxonomic classification of metagenomic sequences with k-mer signatures
RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification
Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies
IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring
CDKAM: a taxonomic classification tool using discriminative k-mers and approximate matching strategies
Parvimonas micra, Peptostreptococcus stomatis, Fusobacterium nucleatum and Akkermansia muciniphila as a four-bacteria biomarker panel of colorectal cancer.
Performance extraction and suitability analysis of multi- and many-core architectures for next generation sequencing secondary analysis
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