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Bandage specifications

Information


Unique identifier OMICS_09013
Name Bandage
Alternative name Bioinformatics Application for Navigating De novo Assembly Graphs Easily
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data LastGraph (Velvet), FASTG (SPAdes) and Trinity.fasta
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Ryan Wick

Publication for Bioinformatics Application for Navigating De novo Assembly Graphs Easily

Bandage citations

 (31)
library_books

Acquisition and dissemination of cephalosporin resistant E. coli in migratory birds sampled at an Alaska landfill as inferred through genomic analysis

2018
Sci Rep
PMCID: 5943298
PMID: 29743625
DOI: 10.1038/s41598-018-25474-w

[…] fferent colours representing different alleles. SRST2-detected AMR genes were queried and visualized against putative plasmid contigs that were assembled with PlasmidSPAdes from select isolates using Bandage. Biocide and metal resistance genes were detected from assembled contigs using BacMetScan, using the experimentally confirmed resistance genes dataset (v1.1), and visualized on putative plasmi […]

library_books

Lignite coal burning seam in the remote Altai Mountains harbors a hydrogen driven thermophilic microbial community

2018
Sci Rep
PMCID: 5928048
PMID: 29712968
DOI: 10.1038/s41598-018-25146-9

[…] ter for Biotechnology Information (NCBI) databases. The 16S ribosomal RNA genes were found in contigs by CheckM. The search for continuations of contigs representing fragments of 16S rRNA genes using Bandage program allowed to link 16S rRNA genes to genome bins where 16S rRNA genes were missing.Signal peptides were predicted using Signal P v.4.1 for Gram-positive bacteria (http://www.cbs.dtu.dk/se […]

library_books

Oxygen minimum zone cryptic sulfur cycling sustained by offshore transport of key sulfur oxidizing bacteria

2018
Nat Commun
PMCID: 5928099
PMID: 29712903
DOI: 10.1038/s41467-018-04041-x

[…] ingle reads were excluded from the analysis. Single library assemblies were performed using SPAdes 3.90 with standard parameters and kmers 21, 33, 55, 77, 99, and 127. Genome binning was performed in Bandage by collecting all contigs linked to the contig that contained the full-length 16S rRNA gene of the SUP05 organism as reconstructed by phyloFlash. The genome completeness for all SUP05 bins was […]

library_books

Multi faceted immunomodulatory and tissue tropic clinical bacterial isolate potentiates prostate cancer immunotherapy

2018
Nat Commun
PMCID: 5913311
PMID: 29686284
DOI: 10.1038/s41467-018-03900-x

[…] alore. The trimmed reads were then used to generate genome assemblies with SPAdes version 3.11.1 using the default parameters for paired-end reads. The resulting assembly graphs were visualized using Bandage. The genome was annotated with Rapid Annotation using Subsystem Technology (RAST) and analyzed and visualized using RAST and Artemis. CP1 was stratified into one of the four major E. coli phyl […]

library_books

Genome analysis of the freshwater planktonic Vulcanococcus limneticus sp. nov. reveals horizontal transfer of nitrogenase operon and alternative pathways of nitrogen utilization

2018
BMC Genomics
PMCID: 5902973
PMID: 29661139
DOI: 10.1186/s12864-018-4648-3

[…] . Contaminating sequences were removed by identifying cyanobacterial contigs with a database of core cyanobacterial genes [] using tBLASTn v2.2.30+ (e-value threshold of 1e− 10) and visualising using Bandage v0.07 [] as previously described []. The final assembly consisted of 160 contigs and is deposited on NCBI GenBank under the accession number NQLA01000000. […]

library_books

The Genome Sequence of “Candidatus Fokinia solitaria”: Insights on Reductive Evolution in Rickettsiales

2018
Genome Biol Evol
PMCID: 5905368
PMID: 29659807
DOI: 10.1093/gbe/evy072

[…] Biosciences Sequel sequencing, obtaining 12,243,617 reads. All PacBio reads and the selected Illumina reads were used to perform a second assembly step using the software Unicycler (). The softwares Bandage () and BLAST were then used to manually perform bioinformatic joins on the result of this second assembly. The obtained genome was annotated using Prokka () followed by extensive manual curati […]

Citations

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Bandage institution(s)
Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia; Department of Computing and Information Systems, University of Melbourne, Parkville, Victoria, Australia

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