ArticleBioinformatics advances2022
kmtricks: efficient and flexible construction of Bloom filters for large sequencing data collections.
Article in Bioinformatics advances, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- MKMC enables reference-free transcriptomic analysis using k-mer representations.bioRxiv : the preprint server for biology · 2026Article
- Kaminari: a frugal colored index for approximateBioinformatics advances · 2026Article
- Acute myeloid leukemia risk stratification in younger and older patients through transcriptomic machine learning models.Scientific reports · 2025Article
- SANS ambages: phylogenomics with abundance-filter, multi-threading, and bootstrapping on amino-acid or genomic sequences.BMC bioinformatics · 2025Article
- Logan: Planetary-Scale Genome Assembly Surveys Life's Diversity.bioRxiv : the preprint server for biology · 2025Article
- SourceApp: A Novel Metagenomic Source Tracking Tool that can Distinguish between Fecal Microbiomes Using Genome-To-Source Associations Benchmarked Against Mixed Input Spike-In Mesocosms.Environmental science & technology · 2025Article
- MUSET: set of utilities for constructing abundance unitig matrices from sequencing data.Bioinformatics (Oxford, England) · 2025Article
- The backpack quotient filter: A dynamic and space-efficient data structure for queryingiScience · 2024Article
- Conway-Bromage-Lyndon (CBL): an exact, dynamic representation of k-mer sets.Bioinformatics (Oxford, England) · 2024Article
- Indexing and searching petabase-scale nucleotide resources.Nature methods · 2024Article
- KaMRaT: a C++ toolkit for k-mer count matrix dimension reduction.Bioinformatics (Oxford, England) · 2024Article
- Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA.Nature computational science · 2024Article
- MetaBIDx: a new computational approach to bacteria identification in microbiomes.Microbiome research reports · 2024Article
- Article
- decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods.Microbiome · 2023Article
- Harmonization of supervised machine learning practices for efficient source attribution of Listeria monocytogenes based on genomic data.BMC genomics · 2023Article
- PSBF:Sensors (Basel, Switzerland) · 2023Article
- Scalable sequence database search using partitioned aggregated Bloom comb trees.Bioinformatics (Oxford, England) · 2023Article
- Themisto: a scalable colored k-mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes.Bioinformatics (Oxford, England) · 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
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Summary: When indexing large collections of short-read sequencing data, a common operation that has now been implemented in several tools (Sequence Bloom Trees and variants, BIGSI) is to construct a collection of Bloom filters, one per sample. Each Bloom filter is used to represent a set of Availability and implementation: https://github.com/tlemane/kmtricks. Supplementary information: Supplementary data are available at
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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.