ArticleGigaScience2015
GenomeTester4: a toolkit for performing basic set operations - union, intersection and complement on k-mer lists.
Article in GigaScience, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
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- Plasmid dynamics driving carbapenemase gene dissemination in healthcare environments: a nationwide analysis of closed Enterobacterales genomes.Nature communications · 2025Article
- Y-mer: a k-mer based method for determining human Y chromosome haplogroups from ultra-low sequencing depth data.Genome biology · 2025Article
- Whole-genome sequencing and bioinformatic tools powered by machine learning to identify antibiotic-resistant genes and virulence factors inMicrobial genomics · 2025Article
- Direct long-read visualization reveals hidden variation in GCH1 gene copy number and precise expansion steps.BMC genomics · 2025Article
- The SHR/Akr Y chromosome reveals repeated turnover of the rat pseudoautosomal region.bioRxiv : the preprint server for biology · 2025Article
- PathoGD: an integrative genomics approach to primer and guide RNA design for CRISPR-based diagnostics.Communications biology · 2025Article
- An explainable machine learning pipeline for prediction of antimicrobial resistance inBioinformatics advances · 2025Article
- A survey of k-mer methods and applications in bioinformatics.Computational and structural biotechnology journal · 2024Review
- GeneToCN: an alignment-free method for gene copy number estimation directly from next-generation sequencing reads.Scientific reports · 2023Article
- A single promoter-TALE system for tissue-specific and tuneable expression of multiple genes in rice.Plant biotechnology journal · 2022Article
- Computational graph pangenomics: a tutorial on data structures and their applications.Natural computing · 2022Article
- Whole-genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming.PLoS computational biology · 2022Article
- Article
- The origin and widespread occurrence of Sli-based self-compatibility in potato.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Article
- A human-specific VNTR in the TRIB3 promoter causes gene expression variation between individuals.PLoS genetics · 2020Article
- KmerGO: A Tool to Identify Group-Specific Sequences WithFrontiers in microbiology · 2020Article
- Method for the Identification of Plant DNA in Food Using Alignment-Free Analysis of Sequencing Reads: A Case Study on Lupin.Frontiers in plant science · 2020Article
- Comparative Subsequence Sets Analysis (CoSSA) is a robust approach to identify haplotype specific SNPs; mapping and pedigree analysis of a potato wart disease resistance genePlant methods · 2019Article
- Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundK-mer-based methods of genome analysis have attracted great interest because they do not require genome assembly and can be performed directly on sequencing reads. Many analysis tasks require one to compare k-mer lists from different sequences to find words that are either unique to a specific sequence or common to many sequences. However, no stand-alone k-mer analysis tool currently allows one to perform these algebraic set operations.
findingsWe have developed the GenomeTester4 toolkit, which contains a novel tool GListCompare for performing union, intersection and complement (difference) set operations on k-mer lists. We provide examples of how these general operations can be combined to solve a variety of biological analysis tasks.
conclusionsGenomeTester4 can be used to simplify k-mer list manipulation for many biological analysis tasks.
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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.