ArticleGigaScience2016
Chromosomer: a reference-based genome arrangement tool for producing draft chromosome sequences.
Article in GigaScience, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
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- Genomic and Acoustic Biogeography of the Iconic Sulphur-crested Cockatoo Clarifies Species Limits and Patterns of Intraspecific Diversity.Molecular biology and evolution · 2024Article
- First draft reference genome and annotation of the alternative oil species Physaria fendleri.G3 (Bethesda, Md.) · 2024Article
- The role of ADAR1 through and beyond its editing activity in cancer.Cell communication and signaling : CCS · 2024Review
- Newly developed genomic SSR markers revealed the population structure and genetic characteristics of abaca (Biotechnologia · 2024Article
- Optimization of the "Ecology and evolution · 2023Article
- Genome-wide characterization of twoAoB PLANTS · 2022Article
- Assembly of complete diploid-phased chromosomes from draft genome sequences.G3 (Bethesda, Md.) · 2022Article
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- SunUp and Sunset genomes revealed impact of particle bombardment mediated transformation and domestication history in papaya.Nature genetics · 2022Article
- Review
- A chromosome-level genome assembly of Cairina moschata and comparative genomic analyses.BMC genomics · 2021Article
- Genome Analysis ofGenes · 2021Article
- Development of Genome-Wide Functional Markers Using Draft Genome Assembly of Guava (Frontiers in plant science · 2021Article
- Comparative Genomics Supports That Brazilian BioethanolFrontiers in microbiology · 2021Article
- HDG-select: A novel GUI based application for gene selection and classification in high dimensional datasets.PloS one · 2021Article
- Improved reconstruction and comparative analysis of chromosome 12 to rectify Mis-assemblies in Gossypium arboreum.BMC genomics · 2020Article
- Whole genome resequencing of four Italian sweet pepper landraces provides insights on sequence variation in genes of agronomic value.Scientific reports · 2020Article
- Parallelism in eco-morphology and gene expression despite variable evolutionary and genomic backgrounds in a Holarctic fish.PLoS genetics · 2020Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAs the number of sequenced genomes rapidly increases, chromosome assembly is becoming an even more crucial step of any genome study. Since de novo chromosome assemblies are confounded by repeat-mediated artifacts, reference-assisted assemblies that use comparative inference have become widely used, prompting the development of several reference-assisted assembly programs for prokaryotic and eukaryotic genomes.
findingsWe developed Chromosomer - a reference-based genome arrangement tool, which rapidly builds chromosomes from genome contigs or scaffolds using their alignments to a reference genome of a closely related species. Chromosomer does not require mate-pair libraries and it offers a number of auxiliary tools that implement common operations accompanying the genome assembly process.
conclusionsDespite implementing a straightforward alignment-based approach, Chromosomer is a useful tool for genomic analysis of species without chromosome maps. Putative chromosome assemblies by Chromosomer can be used in comparative genomic analysis, genomic variation assessment, potential linkage group inference and other kinds of analysis involving contig or scaffold mapping to a high-quality assembly.
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