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Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index

https://doi.org/10.1101/217372
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What this work says

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

inferredcites →https://doi.org/10.1007/978-3-319-56970-3_16openalex-snapshot
Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees
inferredcites →https://doi.org/10.1007/978-3-319-56970-3_17openalex-snapshot
AllSome Sequence Bloom Trees
inferredcites →https://doi.org/10.1007/s002360050048openalex-snapshot
The log-structured merge-tree (LSM-tree)
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
inferredcites →https://doi.org/10.1038/nbt.3442openalex-snapshot
Fast search of thousands of short-read sequencing experiments
inferredcites →https://doi.org/10.1038/nbt.3988openalex-snapshot
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
inferredcites →https://doi.org/10.1038/ng.1028openalex-snapshot
De novo assembly and genotyping of variants using colored de Bruijn graphs
inferredcites →https://doi.org/10.1038/nmeth.1818openalex-snapshot
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
inferredcites →https://doi.org/10.1038/nmeth.3176openalex-snapshot
Fast and sensitive protein alignment using DIAMOND
inferredcites →https://doi.org/10.1093/bioinformatics/btr011openalex-snapshot
A fast, lock-free approach for efficient parallel counting of occurrences of k -mers
inferredcites →https://doi.org/10.1093/bioinformatics/btt214openalex-snapshot
Compressive genomics for protein databases
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/btx636openalex-snapshot
Squeakr: an exact and approximate k -mer counting system
inferredcites →https://doi.org/10.1093/nar/gkr854openalex-snapshot
The sequence read archive: explosive growth of sequencing data
inferredcites →https://doi.org/10.1101/138016openalex-snapshot
Rainbowfish: A Succinct Colored de Bruijn Graph Representation
inferredcites →https://doi.org/10.1145/3035918.3035963openalex-snapshot
A General-Purpose Counting Filter
inferredcites →https://doi.org/10.1145/362686.362692openalex-snapshot
Space/time trade-offs in hash coding with allowable errors
inferredcites →https://doi.org/10.1186/1471-2105-12-1openalex-snapshot
MTML-msBayes: Approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity
inferredcites →https://doi.org/10.1186/s13015-016-0066-8openalex-snapshot
Bloom Filter Trie: an alignment-free and reference-free data structure for pan-genome storage
inferredcites →https://doi.org/10.14778/2350229.2350275openalex-snapshot
Don't thrash
inferredcites →https://doi.org/10.5555/545381.545411openalex-snapshot
Succinct indexable dictionaries with applications to encoding k-ary trees and multisets

What points at this work

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

inferred← citeshttps://doi.org/10.1007/978-3-030-32686-9_21openalex-snapshot
COBS: A Compact Bit-Sliced Signature Index
inferred← citeshttps://doi.org/10.1016/j.csbj.2021.06.047openalex-snapshot
Buffering updates enables efficient dynamic de Bruijn graphs
inferred← citeshttps://doi.org/10.1038/s41587-018-0010-1openalex-snapshot
Ultrafast search of all deposited bacterial and viral genomic data
inferred← citeshttps://doi.org/10.1093/bioinformatics/btab330openalex-snapshot
Topology-based sparsification of graph annotations
inferred← citeshttps://doi.org/10.1093/bioinformatics/bty632openalex-snapshot
Dynamic compression schemes for graph coloring
inferred← citeshttps://doi.org/10.1093/bioinformatics/btz350openalex-snapshot
Building large updatable colored de Bruijn graphs via merging
inferred← citeshttps://doi.org/10.1101/2025.02.02.636161openalex-snapshot
Faster and Scalable Parallel External-Memory Construction of Colored Compacted de Bruijn Graphs with Cuttlefish 3
inferred← citeshttps://doi.org/10.1101/2025.11.23.690050openalex-snapshot
Optimized k -mer search across millions of bacterial genomes on laptops
inferred← citeshttps://doi.org/10.1101/gr.277615.122openalex-snapshot
Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT
inferred← citeshttps://doi.org/10.1186/s13059-018-1535-9openalex-snapshot
SeqOthello: querying RNA-seq experiments at scale
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