The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.
Bandage: interactive visualization of de novo genome assemblies
Open accessAbstract
Summary: Although de novo assembly graphs contain assembled contigs (nodes), the connections between those contigs (edges) are difficult for users to access. Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections. Users can zoom in to specific areas of the graph and interact with it by moving nodes, adding labels, changing colors and extracting sequences. BLAST searches can be performed within the Bandage graphical user interface and the hits are displayed as highlights in the graph. By displaying connections between contigs, Bandage presents new possibilities for analyzing de novo assemblies that are not possible through investigation of contigs alone. Availability and implementation: Source code and binaries are freely available at https://github.com/rrwick/Bandage. Bandage is implemented in C++ and supported on Linux, OS X and Windows. A full feature list and screenshots are available at http://rrwick.github.io/Bandage. Contact: rrwick@gmail.com Supplementary information : Supplementary data are available at Bioinformatics online.
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Cites
BLAST+: architecture and applications
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-421 · Cited by 22,074
Cited by
Assembly of long, error-prone reads using repeat graphs
Kolmogorov, M., Yuan, J., Lin, Y., & Pevzner, P. A. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0072-8 · Cited by 5,986
Using SPAdes De Novo Assembler
Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A., & Korobeynikov, A. (2020) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.102 · Cited by 3,555
The complete sequence of a human genome
Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., Vollger, M. R., Altemose, N., Uralsky, L., Gershman, A., et al. (2022) · Science · doi:10.1126/science.abj6987 · Cited by 3,136
Mobile Genetic Elements Associated with Antimicrobial Resistance
Partridge, S. R., Kwong, S. M., Firth, N., & Jensen, S. O. (2018) · Clinical Microbiology Reviews · doi:10.1128/cmr.00088-17 · Cited by 2,751
A draft human pangenome reference.
Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., et al. (2023) · Nature · doi:10.1038/s41586-023-05896-x · Cited by 1,129
“8.1, (Wick et al., 2015)).”
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Metadata
- Authors
- Wick, R. R., Schultz, M. B., Zobel, J., & Holt, K. E.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-06-22
- Volume
- 31
- Issue
- 20
- Pages
- 3350-3352
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2153325555
- Cited by
- 3,029
- References
- 1
- FWCI
- 17.75
- Type
- journal article
- Language
- en
- Open access
- hybrid
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