Reducing storage requirements for biological sequence comparison

By Michael Roberts, Wayne B. Hayes, Brian R. Hunt, Stephen M. Mount, James A. Yorke. Bioinform., 2004

445 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/4d6dc037b6cf768393f35aa5726a8cda2ff736a9

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In Molecular Biology

Citations in the corpus

Assembling large genomes with single-molecule sequencing and locality-sensitive hashing (2014, background): “The approach can also be viewed as a generalization of minimizers 27 .”
Pangenomics enables genotyping known structural variants in 5,202 diverse genomes (2021, methodology): “Haplotype minimizer seeding is shown in (C): Seeds are identified using an index of minimizers (subsets of sequences of specified length k ) ( 50 ) over the sequences of all the GBWT haplotypes.”
New strategies to improve minimap2 alignment accuracy (2021, background): “Minimap2 keeps all k -mer minimizers (Roberts et al., 2004) during indexing.”
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences (2015, methodology): “Roberts et al. (2004) did not discuss the treatment of such equally good minimizers.”
Improved metagenomic analysis with Kraken 2 (2019, methodology): “We also performed a third parameter sweep, focused on translated search (Kraken 2X), where we looked at values for l in the interval [11, 15], values for k in the interval [l, l+3], and values for s in the interval [0, 3].”
Minimus: a fast, lightweight genome assembler (2007, background): “hash-overlap – a sequence overlapper that uses minimizers [27] to increase speed and decrease memory usage.”
BayesHammer: Bayesian clustering for error correction in single-cell sequencing (2012, unknown): “[15].”
Mash: fast genome and metagenome distance estimation using MinHash (2015, methodology): “[41], which has been used in genome assembly [42], k-mer counting [43], and metagenomics [44].”
Kraken: ultrafast metagenomic sequence classification using exact alignments (2014, methodology): “Because Kraken very frequently uses a k-mer as a database query immediately after querying an adjacent kmer, and because adjacent k-mers share a substantial amount of sequence, we utilize the minimizer concept [20] to group similar k-mers together.”