ArticleBMC bioinformatics2015
Sealer: a scalable gap-closing application for finishing draft genomes.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers.
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Who cites it
78 citing papers in PubMed.
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- Complete genome sequence and functional characterization of Bacillus amyloliquefaciens NJF-55: a sheep-derived probiotic candidate.Scientific reports · 2026Article
- DL-GapFilling: a novel deep learning framework for improved plant genome gap filling.Briefings in bioinformatics · 2026Article
- Shifts in bee diet breadths are associated with gene gains and losses and positive selection across olfactory receptors.G3 (Bethesda, Md.) · 2025Article
- Comparative Genomics and Draft Genome Assembly of the Elite Tunisian Date Palm Cultivar Deglet Nour: Insights into the Genetic Variations Linked to Fruit Ripening and Quality Traits.International journal of molecular sciences · 2025Article
- Synteny Enabled Upgrade of the Galapagos Giant Tortoise Genome Improves Inferences of Runs of Homozygosity.Ecology and evolution · 2025Article
- Identification and Characterization of Innate Immunity in Actinidia melanandra in Response to Pseudomonas syringae pv. actinidiae.Plant, cell & environment · 2025Article
- Whole genome sequencing, assembly and annotation of the Southern Ground Hornbill - Bucorvus leadbeateri.Scientific data · 2025Article
- IMA GENOME - F20 A draft genome assembly ofIMA fungus · 2025Article
- Utilizing Deep Neural Networks to Fill Gaps in Small Genomes.International journal of molecular sciences · 2024Article
- Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response.G3 (Bethesda, Md.) · 2023Article
- Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies.Nature communications · 2023Article
- A few essential genetic loci distinguish Penstemon species with flowers adapted to pollination by bees or hummingbirds.PLoS biology · 2023Article
- High-quality genome assemblies provide clues on the evolutionary advantage of blue peafowl over green peafowl.Heliyon · 2023Article
- MTG-Link: leveraging barcode information from linked-reads to assemble specific loci.BMC bioinformatics · 2023Article
- Comparative Genomic Analysis of Warthog and Sus Scrofa Identifies Adaptive Genes Associated with African Swine Fever.Biology · 2023Article
- RegCloser: a robust regression approach to closing genome gaps.BMC bioinformatics · 2023Article
- Linear time complexity de novo long read genome assembly with GoldRush.Nature communications · 2023Article
- ntLink: A Toolkit for De Novo Genome Assembly Scaffolding and Mapping Using Long Reads.Current protocols · 2023Article
18 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
backgroundWhile next-generation sequencing technologies have made sequencing genomes faster and more affordable, deciphering the complete genome sequence of an organism remains a significant bioinformatics challenge, especially for large genomes. Low sequence coverage, repetitive elements and short read length make de novo genome assembly difficult, often resulting in sequence and/or fragment "gaps" - uncharacterized nucleotide (N) stretches of unknown or estimated lengths. Some of these gaps can be closed by re-processing latent information in the raw reads. Even though there are several tools for closing gaps, they do not easily scale up to processing billion base pair genomes.
resultsHere we describe Sealer, a tool designed to close gaps within assembly scaffolds by navigating de Bruijn graphs represented by space-efficient Bloom filter data structures. We demonstrate how it scales to successfully close 50.8% and 13.8% of gaps in human (3 Gbp) and white spruce (20 Gbp) draft assemblies in under 30 and 27 h, respectively - a feat that is not possible with other leading tools with the breadth of data used in our study.
conclusionSealer is an automated finishing application that uses the succinct Bloom filter representation of a de Bruijn graph to close gaps in draft assemblies, including that of very large genomes. We expect Sealer to have broad utility for finishing genomes across the tree of life, from bacterial genomes to large plant genomes and beyond. Sealer is available for download at https://github.com/bcgsc/abyss/tree/sealer-release.
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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.