ArticleCell systems2018
Mantis: A Fast, Small, and Exact Large-Scale Sequence-Search Index.
Article in Cell systems, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed.
- Article
- LOCALE: Local-Alignment Embeddings for Noise-Robust DNA Search at SRA Scale.bioRxiv : the preprint server for biology · 2026Article
- MegaPX: fast and space-efficient peptide assignment method using IBF-based multi-indexing.Bioinformatics (Oxford, England) · 2026Article
- Fast and Scalable Parallel External-Memory Construction of Colored Compacted de Bruijn Graphs with Cuttlefish 3.bioRxiv : the preprint server for biology · 2025Article
- Movi Color: fast and accurate taxonomic classification with the move structure.ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- Where the Patterns Are: Repetition-Aware Compression for Colored de Bruijn GraphsJournal of computational biology : a journal of computational molecular cell biology · 2024Article
- Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters.Genome research · 2024Article
- Label-guided seed-chain-extend alignment on annotated De Bruijn graphs.Bioinformatics (Oxford, England) · 2024Article
- Indexing and searching petabase-scale nucleotide resources.Nature methods · 2024Article
- Extremely fast construction and querying of compacted and colored de Bruijn graphs with GGCAT.Genome research · 2023Article
- Matchtigs: minimum plain text representation of k-mer sets.Genome biology · 2023Article
- Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries.Genome biology · 2023Article
- MetaProFi: an ultrafast chunked Bloom filter for storing and querying protein and nucleotide sequence data for accurate identification of functionally relevant genetic variants.Bioinformatics (Oxford, England) · 2023Article
- KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping.Bioinformatics (Oxford, England) · 2023Article
- Strain level microbial detection and quantification with applications to single cell metagenomics.Nature communications · 2022Article
- Scalable, ultra-fast, and low-memory construction of compacted de Bruijn graphs with Cuttlefish 2.Genome biology · 2022Article
- Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments.Bioinformatics (Oxford, England) · 2022Article
- SPRISS: approximating frequent k-mers by sampling reads, and applications.Bioinformatics (Oxford, England) · 2022Article
- An incrementally updatable and scalable system for large-scale sequence search using the Bentley-Saxe transformation.Bioinformatics (Oxford, England) · 2022Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Sequence-level searches on large collections of RNA sequencing experiments, such as the NCBI Sequence Read Archive (SRA), would enable one to ask many questions about the expression or variation of a given transcript in a population. Existing approaches, such as the sequence Bloom tree, suffer from fundamental limitations of the Bloom filter, resulting in slow build and query times, less-than-optimal space usage, and potentially large numbers of false-positives. This paper introduces Mantis, a space-efficient system that uses new data structures to index thousands of raw-read experiments and facilitates large-scale sequence searches. In our evaluation, index construction with Mantis is 6× faster and yields a 20% smaller index than the state-of-the-art split sequence Bloom tree (SSBT). For queries, Mantis is 6-108× faster than SSBT and has no false-positives or -negatives. For example, Mantis was able to search for all 200,400 known human transcripts in an index of 2,652 RNA sequencing experiments in 82 min; SSBT took close to 4 days.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.