Mash: fast genome and metagenome distance estimation using MinHash
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Summary
Mash extends the MinHash dimensionality-reduction technique to include a pairwise mutation distance and P value significance test, enabling the efficient clustering and search of massive sequence collections.
- Type
- preprint
- Published
- 2015-10-26
- Cited by
- 2,939
- References
- 67
- Access
- Open access
- OpenAlex
- https://openalex.org/W2293903575
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:2107688
Keywords
RefSeq, Metagenomics, Cluster analysis, Computational biology, Nanopore sequencing
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- A Preprocessor for Shotgun Assembly of Large Genomes
- The power of simple tabulation hashing
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- Approximate String Matching with q-grams and Maximal Matches
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- Near Duplicate Image Detection: min-Hash and tf-idf Weighting
- Alignment-free phylogenetics and population genetics
- An Algorithm for Drawing General Undirected Graphs
- Compareads: comparing huge metagenomic experiments
Cited by
- Genomic Analysis of Shewanella sp. O23S—The Natural Host of the pSheB Plasmid Carrying Genes for Arsenic Resistance and Dissimilatory Reduction
- Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11,087 Clinical Isolates
- Pseudoalignment for metagenomic read assignment
- StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees
- Computational prospecting the great viral unknown.
- Multiple comparative metagenomics using multiset k-mer counting
- In Situ Replication Rates for Uncultivated Bacteria in Microbial Communities
- Partial recovery of microbiomes after antibiotic treatment
- Evaluation of Matrix-Assisted Laser Desorption Ionization−Time of Flight Mass Spectrometry for Identification of Mycobacterium abscessus Subspecies According to Whole-Genome Sequencing
- Determining the cause of recurrent Clostridium difficile infection using whole genome sequencing.
- Measurement of bacterial replication rates in microbial communities
- The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community
- Species Mash-up
- Assembling the microbial dark matter
- Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations
- The Role of Ocean Currents in the Temperature Selection of Plankton: Insights from an Individual-Based Model
- MinION as part of a biomedical rapidly deployable laboratory.
- A brief primer on genomic epidemiology: lessons learned from Mycobacterium tuberculosis
- Experimental warming reveals positive feedbacks to climate change in the Eurasian Steppe
- An advanced reference genome of Trifolium subterraneum L. reveals genes related to agronomic performance
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