ArticlePLoS computational biology2022
The SAMBA tool uses long reads to improve the contiguity of genome assemblies.
Article in PLoS computational biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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35 citing papers in PubMed.
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- Draft hybrid genome assembly of the photosynthetic sacoglossan Elysia crispata provides insights into sacoglossan biology.BMC genomics · 2026Article
- Hybrid Whole-Genome Sequencing ofInternational journal of molecular sciences · 2026Article
- A reference genome sequence for the exceptionally long-lived Great Basin bristlecone pine, Pinus longaeva.G3 (Bethesda, Md.) · 2026Article
- Integrative genomic, transcriptomic, and metabolomic profiling of Dillenia suffruticosa.Scientific reports · 2026Article
- Automatic Generation of Model Sequences for Complex Regions in Assembly Graphs.bioRxiv : the preprint server for biology · 2026Article
- Comparative Genomics and Phylogenomics of the Mustelinae Lineage (Mustelidae, Carnivora).Genome biology and evolution · 2026Article
- Genome sequencing uncovers the history of the Russian desman's gradual population decline and contributes to the evolutionary history of Talpidae.BMC ecology and evolution · 2026Article
- DL-GapFilling: a novel deep learning framework for improved plant genome gap filling.Briefings in bioinformatics · 2026Article
- Comprehensive whole genome hybrid assembly unravels genes and secretome ofFrontiers in fungal biology · 2026Article
- Exploration of inactive metabolic pathways in AntarcticIMA fungus · 2026Article
- Benchmarking genome assemblers for four bacterial models based on contiguity, correctness, and completeness.Scientific reports · 2025Article
- Assembling genomes of non-model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae).The Plant journal : for cell and molecular biology · 2025Article
- TRFill: synergistic use of HiFi and Hi-C sequencing enables accurate assembly of tandem repeats for population-level analysis.Genome biology · 2025Article
- Evolutionary history of magnoliid genomes and benzylisoquinoline alkaloid biosynthesis.Nature communications · 2025Article
- Three reference genomes for freshwater diatom ecology and evolution.Journal of phycology · 2025Article
- Genome Assembly, Polishing, and Analysis of the Chytrid Batrachochytrium salamandrivorans.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Inter-chromosomal transcription hubs shape the 3D genome architecture of African trypanosomes.Nature communications · 2024Article
- A reference quality, fully annotated diploid genome from a Saudi individual.Scientific data · 2024Article
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2 authors.
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Abstract
Third-generation sequencing technologies can generate very long reads with relatively high error rates. The lengths of the reads, which sometimes exceed one million bases, make them invaluable for resolving complex repeats that cannot be assembled using shorter reads. Many high-quality genome assemblies have already been produced, curated, and annotated using the previous generation of sequencing data, and full re-assembly of these genomes with long reads is not always practical or cost-effective. One strategy to upgrade existing assemblies is to generate additional coverage using long-read data, and add that to the previously assembled contigs. SAMBA is a tool that is designed to scaffold and gap-fill existing genome assemblies with additional long-read data, resulting in substantially greater contiguity. SAMBA is the only tool of its kind that also computes and fills in the sequence for all spanned gaps in the scaffolds, yielding much longer contigs. Here we compare SAMBA to several similar tools capable of re-scaffolding assemblies using long-read data, and we show that SAMBA yields better contiguity and introduces fewer errors than competing methods. SAMBA is open-source software that is distributed at https://github.com/alekseyzimin/masurca.
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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.