ArticleMolecular ecology resources2025
Klumpy: A tool to evaluate the integrity of long-read genome assemblies and illusive sequence motifs.
Article in Molecular ecology resources, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Museum specimens reveal the genomic consequences of long-term population decline in an insect pollinator.Molecular biology and evolution · 2026Article
- A new phased assembly of the Antarctic spiny plunderfish provides novel insights into the evolution of the notothenioid radiation.bioRxiv : the preprint server for biology · 2026Article
- Chromosomal rearrangements and segmental deletions contribute to gene loss in squamates.BMC biology · 2026Article
- Troubleshooting common errors in assemblies of long-read metagenomes.Nature biotechnology · 2026Article
- Editorial 2026.Molecular ecology resources · 2026Article
- Illuminating the mystery of thylacine extinction: a role for relaxed selection and gene loss.Proceedings. Biological sciences · 2025Article
- CloseRead: a tool for assessing assembly errors in immunoglobulin loci applied to vertebrate long-read genome assemblies.Genome biology · 2025Article
- Common Ancestry of the Id Locus: Chromosomal Rearrangement and Polygenic Possibilities.Journal of molecular evolution · 2025Article
- The genome of the cryopelagic Antarctic bald notothen, Trematomus borchgrevinki.G3 (Bethesda, Md.) · 2025Article
- Klumpy: A tool to evaluate the integrity of long-read genome assemblies and illusive sequence motifs.Molecular ecology resources · 2025Article
- Genomic Validation of PERV-C-Free Pigs to Support Xenotransplantation.XenotransplantationArticle
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The improvement and decreasing costs of third-generation sequencing technologies has widened the scope of biological questions researchers can address with de novo genome assemblies. With the increasing number of reference genomes, validating their integrity with minimal overhead is vital for establishing confident results in their applications. Here, we present Klumpy, a tool for detecting and visualizing both misassembled regions in a genome assembly and genetic elements (e.g. genes) of interest in a set of sequences. By leveraging the initial raw reads in combination with their respective genome assembly, we illustrate Klumpy's utility by investigating antifreeze glycoprotein (afgp) loci across two icefishes, by searching for a reported absent gene in the northern snakehead fish, and by scanning the reference genomes of a mudskipper and bumblebee for misassembled regions. In the two former cases, we were able to provide support for the noncanonical placement of an afgp locus in the icefishes and locate the missing snakehead gene. Furthermore, our genome scans were able identify an unmappable locus in the mudskipper reference genome and identify a putative repetitive element shared among several species of bees.
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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 Socratic graph.