The DOI matches its Crossref record; 49 of the 49 references it cites were found in a registry or an index.
BlobToolKit – Interactive Quality Assessment of Genome Assemblies
Open accessAbstract
Reconstruction of target genomes from sequence data produced by instruments that are agnostic as to the species-of-origin may be confounded by contaminant DNA. Whether introduced during sample processing or through co-extraction alongside the target DNA, if insufficient care is taken during the assembly process, the final assembled genome may be a mixture of data from several species. Such assemblies can confound sequence-based biological inference and, when deposited in public databases, may be included in downstream analyses by users unaware of underlying problems. We present BlobToolKit, a software suite to aid researchers in identifying and isolating non-target data in draft and publicly available genome assemblies. BlobToolKit can be used to process assembly, read and analysis files for fully reproducible interactive exploration in the browser-based Viewer. BlobToolKit can be used during assembly to filter non-target DNA, helping researchers produce assemblies with high biological credibility. We have been running an automated BlobToolKit pipeline on eukaryotic assemblies publicly available in the International Nucleotide Sequence Data Collaboration and are making the results available through a public instance of the Viewer at https://blobtoolkit.genomehubs.org/view. We aim to complete analysis of all publicly available genomes and then maintain currency with the flow of new genomes. We have worked to embed these views into the presentation of genome assemblies at the European Nucleotide Archive, providing an indication of assembly quality alongside the public record with links out to allow full exploration in the Viewer.
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Cited by
Significantly improving the quality of genome assemblies through curation
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Sequence locally, think globally: the Darwin Tree of Life Project
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Self-citationRapid and sensitive detection of genome contamination at scale with FCS-GX
Astashyn, A., Tvedte, E. S., Sweeney, D., Sapojnikov, V., Bouk, N., Joukov, V., Mozes, E., Strope, P. K., Sylla, P. M., Wagner, L., et al. (2024) · Genome Biology · doi:10.1186/s13059-024-03198-7 · Cited by 469
compleasm: a faster and more accurate reimplementation of BUSCO
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Metadata
- Authors
- Challis, R., Richards, E., Rajan, J., Cochrane, G., & Blaxter, M.
- Venue
- G3 Genes|Genomes|Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-04-01
- Volume
- 10
- Issue
- 4
- Pages
- 1361-1374
- ISSN
- 2160-1836 (ISSN-L)
- OpenAlex
- W3007075333
- Cited by
- 2,610
- References
- 49
- FWCI
- 50.07
- Type
- journal article
- Language
- en
- Open access
- gold
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