ArticleGenome biology2020
iMOKA: k-mer based software to analyze large collections of sequencing data.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- MKMC enables reference-free transcriptomic analysis using k-mer representations.bioRxiv : the preprint server for biology · 2026Article
- Reference-free RNA profiling predicts triple negative breast cancer chemoresistance to neoadjuvant treatment.NAR cancer · 2025Article
- From nucleotides to numbers: a comprehensive review of RNA feature extraction methods for computational modelling.Briefings in bioinformatics · 2025Review
- Identification of potential SARS-CoV-2 genomic regions representing hallmarks for adaptation to different hosts.iMetaOmics · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- SHARK enables sensitive detection of evolutionary homologs and functional analogs in unalignable and disordered sequences.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- KaMRaT: a C++ toolkit for k-mer count matrix dimension reduction.Bioinformatics (Oxford, England) · 2024Article
- Species annotation using a k-mer based KNN model.Bioinformation · 2024Article
- Unsupervised machine learning framework for discriminating major variants of concern during COVID-19.PloS one · 2023Article
- Predicting emerging SARS-CoV-2 variants of concern through a One Class dynamic anomaly detection algorithm.BMJ health & care informatics · 2022Article
- Chimeric RNAs Discovered by RNA Sequencing and Their Roles in Cancer and Rare Genetic Diseases.Genes · 2022Review
- The contribution of uncharted RNA sequences to tumor identity in lung adenocarcinoma.NAR cancer · 2022Article
- iMOKA: k-mer based software to analyze large collections of sequencing data.Genome biology · 2020Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
iMOKA (interactive multi-objective k-mer analysis) is a software that enables comprehensive analysis of sequencing data from large cohorts to generate robust classification models or explore specific genetic elements associated with disease etiology. iMOKA uses a fast and accurate feature reduction step that combines a Naïve Bayes classifier augmented by an adaptive entropy filter and a graph-based filter to rapidly reduce the search space. By using a flexible file format and distributed indexing, iMOKA can easily integrate data from multiple experiments and also reduces disk space requirements and identifies changes in transcript levels and single nucleotide variants. iMOKA is available at https://github.com/RitchieLabIGH/iMOKA and Zenodo https://doi.org/10.5281/zenodo.4008947 .
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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.