A Fast and Symmetric DUST Implementation to Mask Low-Complexity DNA Sequences

By Aleksandr Morgulis, E. Gertz, Alejandro A. Schäffer, Richa Agarwala. J. Comput. Biol., 2006

500 citations recorded by the source corpus.

Subfields: Artificial Intelligence, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/8441a9540d65ae12401db5bf14de727a518bf2cd

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Citations in the corpus

Variant interpretation using population databases: lessons from gnomAD (2021, background): “The LCR flag highlights variants identified in these regions to allow a more careful review (Morgulis et al., 2006).”
Petabase-scale sequence alignment catalyses viral discovery (2020, methodology): “0.667) 54 and masked by Dustmasker (ncbi-blast:2.10.0) ( --window 30 and --window 64 ) 55 .”
Database indexing for production MegaBLAST searches (2008, methodology): “However, for an unmasked database and query, the indexed search may actually have worse performance compared to the non-indexed case, if the query contains highly repetitive regions.”
Metagenomics: Tools and Insights for Analyzing Next-Generation Sequencing Data Derived from Biodiversity Studies (2015, methodology): “Most of these tools make use of Phred or Q quality scores, 80,81 the thresholds of which depend on sequencing technology; 2) Masking of low-complexity reads performed using tools such as DUST 82 ; 3) A de-replication step that removes sequences that are more than 95% identical; 4) A screening step p”
Landscape of multi-nucleotide variants in 125,748 human exomes and 15,708 genomes (2020, methodology): “We also ﬁ ltered out variant sites that are classi ﬁ ed as low-complexity regions (LCRs) identi ﬁ ed with the symmetric DUST algorithm 56 at a score threshold of 30, and additionally applied adjusted threshold criteria (GQ ≥ 20, DP ≥ 10, and allele balance>0.2 for heterozygote genotypes) for ﬁ…”
The Ensembl gene annotation system (2016, methodology): “RepeatMasker (57), Dust (58) and Tandem Repeat Finder (59) (TRF) are used to mask repetitive genomic sequence.”
Improved metagenomic analysis with Kraken 2 (2019, methodology): “…values for ℓ in the interval [25, 31], values for k in the interval [ ℓ , ℓ + 10], and values for s in the interval [0, 7]; the second parameter sweep looked at values of ℓ in the interval [25, 31], fixed k = ℓ , values for f in the set {0.125, 0.25, 0.5}, and values for s in the interval [0, 7].”
A new repeat-masking method enables specific detection of homologous sequences (2010, methodology): “TANTAN used 78 s to mask the 100-megabase C. elegans genome, whereas DUSTMASKER used 18 s and TRF used 677 s (on a Xeon E5540 CPU).”
The design and construction of reference pangenome graphs with minigraph (2020, methodology): “nnotate VNTRs with long motifs. It also often interprets VNTRs as impure STRs. Therefore, we did not use the RepeatMasker VNTR or STR annotations directly. Instead, we combined RepeatMasker and SDUST [56] results to collect low-complexity regions (LCRs). We identied pure tandem repeats composed of a”
Genome-wide mapping of alternative splicing in Arabidopsis thaliana. (2010, methodology): “A filter similar to DUST (Morgulis et al. 2006) and implemented in Perl (http://bioperl.org/pipermail/ bioperl-l/1999-November/003313.html) to remove reads containing low-complexity stretches.”