Bandage: interactive visualisation of de novo genome assemblies

Wick, Ryan R.; Schultz, Mark B.; Zobel, Justin; Holt, Kathryn E.

doi:10.1101/018333

Cited by 418 publications

(463 citation statements)

References 7 publications

(8 reference statements)

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“…We used chloroplast genome of Rheum palmatum (accession number: KR816224) (Fan et al 2015) as a reference sequence to align the contigs and identify gaps. To fill the gap, Price (Ruby et al 2013) and MITObim v1.8 (Hahn et al 2013) were applied, and Bandage (Wick et al 2015) was used to identify the borders of the IR, LSC, and SSC regions. The complete sequence was primarily annotated by Geseq (Tillich et al 2017) and Plann combined with manual correction.…”

Section: Mitogenome Announcementmentioning

confidence: 99%

Characterization of the complete chloroplast genome of sorrel (Rumex acetosa)

Gui

Jiang

Wang

et al. 2018

Mitochondrial DNA Part B

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Rumex acetosa , known as sheep’s sorrel, red sorrel, sour weed, and field sorrel, is a species of flowering plant in the buckwheat family Polygonaceae. In this study, the complete chloroplast (cp) genome of R. acetosa (Rumiceae) was determined through Illumina sequencing method. The complete chloroplast genome of R. acetosa was 160,269 bp in length and contained a pair of IR regions (30,503 bp) separated by a small single copy region (13,128 bp) and a large single copy region (86,135 bp). This cp genome is encoded with 129 genes including 83 protein-coding genes, 36 tRNA genes, and 8 ribosomal RNA genes. The overall GC content of R. acetosa cp genome is 37.2%. By phylogenetic analysis using Bayesian method, R. acetosa showed the closest relationship with other 2 Rumiceae species, Rheum palmatum and Oxyria sinensis .

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Section: Mitogenome Announcementmentioning

confidence: 99%

Characterization of the complete chloroplast genome of sorrel (Rumex acetosa)

Gui

Jiang

Wang

et al. 2018

Mitochondrial DNA Part B

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“…Manual editing can e.g. be done using Bandage (Wick et al, 2015), which allows to modify a graph by interacting with its graphical user interface. However, Bandage does not record the operations applied to the graph.…”

Section: Comparison Of Gfa Graphs and Generation Of Edit Scriptsmentioning

confidence: 99%

“…The original assembly graph of the fosmid data as delivered by SPAdes (a) and the simplifications obtained by RGFATools (b,c,d). The figure was prepared using Bandage (Wick et al, 2015).…”

Section: /9mentioning

confidence: 99%

“…ADP1 containing a CRISP with 6 instances of a 28 bp repeat (R), one of which containing a mismatch (R') and 32 bp long spacers (S1 to S5). The figure was prepared using Bandage (Wick et al, 2015).…”

Section: /9mentioning

confidence: 99%

“…The format conversion tool gfatools (http://github.com/lh3/gfatools) allows to convert the graphs of Velvet (Zerbino and Birney, 2008), SPAdes, Soapdenovo (Luo et al, 2012), and SGA (Simpson and Durbin, 2012) to GFA. Manual GUI-based editing of a GFA graph is possible using Bandage (Wick et al, 2015). However, neither Bandage, nor any other of the mentioned tools offer scripting capability or an application programming interface to their GFA implementation.…”

Section: /9mentioning

confidence: 99%

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RGFA: powerful and convenient handling of assembly graphs

Gonnella

Kurtz

2016

Preprint

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The "Graphical Fragment Assembly" (GFA) is an emerging format for the representation of sequence assembly graphs, which can be adopted by both de Bruijn graph-and string graph-based assemblers. Here we present RGFA, an implementation of the proposed GFA specification in Ruby. It allows to conveniently parse, edit and write GFA files. Complex operations such as the separation of the implicit instances of repeats and the merging of linear paths can be performed. A typical application of RGFA is the editing of a graph, to finish the assembly of a sequence, using information not available to the assembler. We illustrate a use case, in which the assembly of a repetitive metagenomic fosmid insert was completed using a script based on RGFA. Furthermore, we show how the API provided by RGFA allows to design complex graph editing algorithms. As an example, we developed a detection algorithm for CRISPRs in a de Bruijn graph. Finally, RGFA can be used for comparing assembly graphs, e.g. to document the changes in a graph after applying a GUI editor. A program, GFAdiff is provided, which compares the information in two graphs, and generate a report or a Ruby script documenting the transformation steps between the graphs.

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Using SPAdes De Novo Assembler

Prjibelski

Antipov

Meleshko

et al. 2020

CP in Bioinformatics

1,271

812

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SPAdes—St. Petersburg genome Assembler—was originally developed for de novo assembly of genome sequencing data produced for cultivated microbial isolates and for single‐cell genomic DNA sequencing. With time, the functionality of SPAdes was extended to enable assembly of IonTorrent data, as well as hybrid assembly from short and long reads (PacBio and Oxford Nanopore). In this article we present protocols for five different assembly pipelines that comprise the SPAdes package and that are used for assembly of metagenomes and transcriptomes as well as assembly of putative plasmids and biosynthetic gene clusters from whole‐genome sequencing and metagenomic datasets. In addition, we present guidelines for understanding results with use cases for each pipeline, and several additional support protocols that help in using SPAdes properly. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Assembling isolate bacterial datasets Basic Protocol 2: Assembling metagenomic datasets Basic Protocol 3: Assembling sets of putative plasmids Basic Protocol 4: Assembling transcriptomes Basic Protocol 5: Assembling putative biosynthetic gene clusters Support Protocol 1: Installing SPAdes Support Protocol 2: Providing input via command line Support Protocol 3: Providing input data via YAML format Support Protocol 4: Restarting previous run Support Protocol 5: Determining strand‐specificity of RNA‐seq data

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Bandage: interactive visualisation of de novo genome assemblies

Cited by 418 publications

References 7 publications

Characterization of the complete chloroplast genome of sorrel (Rumex acetosa)

Characterization of the complete chloroplast genome of sorrel (Rumex acetosa)

RGFA: powerful and convenient handling of assembly graphs

Using SPAdes De Novo Assembler

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