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Improving on hash-based probabilistic sequence classification using multiple spaced seeds and multi-index Bloom filters

https://doi.org/10.1101/434795
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/spe.2198openalex-snapshot
Optimized succinct data structures for massive data
inferredcites →https://doi.org/10.1016/j.csl.2009.12.001openalex-snapshot
Recursive n-gram hashing is pairwise independent, at best
inferredcites →https://doi.org/10.1016/j.dam.2018.03.035openalex-snapshot
A resource-frugal probabilistic dictionary and applications in bioinformatics
inferredcites →https://doi.org/10.1038/srep19233openalex-snapshot
An evaluation of the accuracy and speed of metagenome analysis tools
inferredcites →https://doi.org/10.1080/01621459.1961.10482090openalex-snapshot
Multiple Comparisons Among Means
inferredcites →https://doi.org/10.1089/cmb.2014.0173openalex-snapshot
A Coverage Criterion for Spaced Seeds and Its Applications to Support Vector Machine String Kernels and k -Mer Distances
inferredcites →https://doi.org/10.1093/bioinformatics/18.3.440openalex-snapshot
PatternHunter: faster and more sensitive homology search
inferredcites →https://doi.org/10.1093/bioinformatics/btm422openalex-snapshot
Multiple spaced seeds for homology search
inferredcites →https://doi.org/10.1093/bioinformatics/btq230openalex-snapshot
Classification of DNA sequences using Bloom filters
inferredcites →https://doi.org/10.1093/bioinformatics/btr368openalex-snapshot
SpEED: fast computation of sensitive spaced seeds
inferredcites →https://doi.org/10.1093/bioinformatics/bts187openalex-snapshot
pIRS: Profile-based Illumina pair-end reads simulator
inferredcites →https://doi.org/10.1093/bioinformatics/btu558openalex-snapshot
BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters
inferredcites →https://doi.org/10.1093/bioinformatics/btv419openalex-snapshot
Spaced seeds improve k -mer-based metagenomic classification
inferredcites →https://doi.org/10.1093/bioinformatics/btw397openalex-snapshot
ntHash: recursive nucleotide hashing
inferredcites →https://doi.org/10.1093/bioinformatics/btw542openalex-snapshot
Higher classification sensitivity of short metagenomic reads with CLARK- S
inferredcites →https://doi.org/10.1093/bioinformatics/btw832openalex-snapshot
ntCard: a streaming algorithm for cardinality estimation in genomics data
inferredcites →https://doi.org/10.1093/bioinformatics/btx432openalex-snapshot
A novel data structure to support ultra-fast taxonomic classification of metagenomic sequences with k-mer signatures
inferredcites →https://doi.org/10.1093/bioinformatics/bty292openalex-snapshot
A space and time-efficient index for the compacted colored de Bruijn graph
inferredcites →https://doi.org/10.1093/nar/gkv1189openalex-snapshot
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
inferredcites →https://doi.org/10.1093/nar/gkw1121openalex-snapshot
COSMIC: somatic cancer genetics at high-resolution
inferredcites →https://doi.org/10.1109/tnet.2018.2820067openalex-snapshot
Memory-Efficient and Ultra-Fast Network Lookup and Forwarding Using Othello Hashing
inferredcites →https://doi.org/10.1142/s0219720004000661openalex-snapshot
PATTERNHUNTER II: HIGHLY SENSITIVE AND FAST HOMOLOGY SEARCH
inferredcites →https://doi.org/10.1142/s0219720006001977openalex-snapshot
A UNIFYING FRAMEWORK FOR SEED SENSITIVITY AND ITS APPLICATION TO SUBSET SEEDS
inferredcites →https://doi.org/10.1145/210089.210111openalex-snapshot
Algorithm 748: enclosing zeros of continuous functions
inferredcites →https://doi.org/10.1145/3147.3165openalex-snapshot
Random sampling with a reservoir
inferredcites →https://doi.org/10.1145/362686.362692openalex-snapshot
Space/time trade-offs in hash coding with allowable errors
inferredcites →https://doi.org/10.1186/1471-2105-14-69openalex-snapshot
BOND: Basic OligoNucleotide Design
inferredcites →https://doi.org/10.1186/gb-2014-15-3-r46openalex-snapshot
Kraken: ultrafast metagenomic sequence classification using exact alignments
inferredcites →https://doi.org/10.1186/s12864-015-1419-2openalex-snapshot
CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers
inferredcites →https://doi.org/10.1186/s13059-018-1535-9openalex-snapshot
SeqOthello: querying RNA-seq experiments at scale
inferredcites →https://doi.org/10.1214/aoms/1177706374openalex-snapshot
Estimation of the Medians for Dependent Variables
inferredcites →https://doi.org/10.1371/journal.pcbi.1003711openalex-snapshot
Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features
inferredcites →https://doi.org/10.1371/journal.pcbi.1005107openalex-snapshot
rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison
inferredcites →https://doi.org/10.14778/2350229.2350275openalex-snapshot
Don't thrash
inferredcites →https://doi.org/10.4230/lipics.sea.2017.25openalex-snapshot
Fast and Scalable Minimal Perfect Hashing for Massive Key Sets
inferredcites →https://doi.org/10.6084/m9.figshare.963153.v1openalex-snapshot
Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1093/nar/gkaa265openalex-snapshot
To Petabytes and beyond: recent advances in probabilistic and signal processing algorithms and their application to metagenomics
inferred← citeshttps://doi.org/10.1145/3445967openalex-snapshot
Data Structures to Represent a Set of k -long DNA Sequences
inferred← citeshttps://doi.org/10.14288/1.0387155openalex-snapshot
Improving sequence analysis with probabilistic data structures and algorithms
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