--- name: "Bandage" section: "1" platform: "linux" package: "bandage" version: "0.9.0-2+b1" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bandage" --- # Bandage(1) Bioinformatics Application for Navigating De novo Assembly Graphs Easily ## NAME Bandage - Bioinformatics Application for Navigating De novo Assembly Graphs Easily ## SYNOPSIS **Bandage** *\* \[*options*\] ## DESCRIPTION Bandage is a GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others.. ## OPTIONS ### Commands - \ Launch the Bandage GUI - load Launch the Bandage GUI and load a graph file - info Display information about a graph - image Generate an image file of a graph - querypaths Output graph paths for BLAST queries - reduce Save a subgraph of a larger graph ### Options - **--help** View this help message - **--helpall** View all command line settings - **--version** View Bandage version number ### Settings The following options configure the Bandage settings that are available in the Bandage GUI. - Colours can be specified using hex values, with or without an alpha channel, (e.g. #FFB6C1 or #7FD2B48C) or using standard colour names (e.g. red, yellowgreen or skyblue). Note that hex colours will either need to be enclosed in quotes (e.g. "#FFB6C1") or have the hash symbol escaped (e.g. \\#FFB6C1). **Graph scope** These settings control the graph scope. If the aroundnodes scope is used, then the **--nodes** option must also be used. If the aroundblast scope is used, a BLAST query must be given with the **--query** option - **--scope** \ Graph scope, from one of the following options: entire, aroundnodes, aroundblast, depthrange (default: entire) - **--nodes** \ A comma-separated list of starting nodes for the aroundnodes scope (default: none) - **--partial** Use partial node name matching (default: exact node name matching) - **--distance** \ The number of node steps away to draw for the aroundnodes and aroundblast scopes (0 to 100, default: 0) - **--mindepth** \ The minimum allowed depth for the depthrange scope (0 to 1e+6, default: 10) - **--maxdepth** \ The maximum allowed depth for the depthrange scope (0 to 1e+6, default: 100) - **--double** Draw graph in double mode (default: off) **Graph size** - **--nodelen** \ Node length per megabase (0 to 1e+6, default: auto) - **--minnodlen** \ Minimum node length (1 to 100, default: 5) - **--edgelen** \ Edge length (0.1 to 100, default: 5) - **--edgewidth** \ Edge width (0.1 to 100, default: 1.5) - **--doubsep** \ Double mode separation (0 to 100, default: 2) **Graph layout** - **--nodseglen** \ Node segment length (1 to 1000, default: 20) - **--iter** \ Graph layout iterations (0 to 4, default: 2) - **--linear** Linear graph layout (default: off) **Graph appearance** - **--edgecol** \ Colour for edges (default: black) - **--outcol** \ Node outline thickness (0 to 100, default: 0) - **--selcol** \ Colour for selections (default: blue) - **--noaa** Disable antialiasing (default: antialiasing on) - **--singlearr** Show node arrowheads in single mode (default: nodes are only displayed with arrowheads in double mode) **Text appearance** - **--textcol** \ Colour for label text (default: black) - **--toutcol** \ Colour for text outline (default: white) - **--toutline** \ Surround text with an outline with this thickness (0 to 10, default: 1.5) - **--centre** Node labels appear at the centre of the node (default: off, node labels appear over visible parts of nodes) **Node width** Node widths are determined using the following formula: - a\*b\*((c/d)^e-1)+1 - a = average node width - b = depth effect on width - c = node depth - d = mean depth - e = power of depth effect on width - **--nodewidth** \ Average node width (0.5 to 1000, default: 5) - **--depwidth** \ Depth effect on width (0 to 1, default: 0.5) - **--deppower** \ Power of depth effect on width (0 to 1, default: 0.5) **Node labels** - **--names** Label nodes with name (default: off) - **--lengths** Label nodes with length (default: off) - **--depth** Label nodes with depth (default: off) - **--blasthits** Label BLAST hits (default: off) - **--fontsize** \ Font size for node labels (1 to 100, default: 12) **Node colours** - **--colour** \ Node colouring scheme, from one of the following options: random, uniform, depth, blastsolid, blastrainbow (default: random if **--query** option not used, blastsolid if **--query** option used) **Random colour scheme** These settings only apply when the random colour scheme is used. - **--ransatpos** \ Positive node saturation (0 to 255, default: 127) - **--ransatneg** \ Negative node saturation (0 to 255, default: 127) - **--ranligpos** \ Positive node lightness (0 to 255, default: 150) - **--ranligneg** \ Negative node lightness (0 to 255, default: 90) - **--ranopapos** \ Positive node opacity (0 to 255, default: 255) - **--ranopaneg** \ Negative node opacity (0 to 255, default: 255) **Uniform colour scheme** These settings only apply when the uniform colour scheme is used. - **--unicolpos** \ Positive node colour (default: firebrick) - **--unicolneg** \ Negative node colour (default: maroon) - **--unicolspe** \ Special node colour (default: green) **Depth colour scheme** These settings only apply when the depth colour scheme is used. - **--depcollow** \ Colour for nodes with depth below the low depth value (default: black) - **--depcolhi** \ Colour for nodes with depth above the high depth value (default: red) - **--depvallow** \ Low depth value (0 to 1e+6, default: auto) - **--depvalhi** \ High depth value (0 to 1e+6, default: auto) **BLAST search** - **--query** \ A FASTA file of either nucleotide or protein sequences to be used as BLAST queries (default: none) - **--blastp** \ Parameters to be used by blastn and tblastn when conducting a BLAST search in Bandage (default: none). Format BLAST parameters exactly as they would be used for blastn/tblastn on the command line, and enclose them in quotes. - **--alfilter** \ Alignment length filter for BLAST hits. Hits with shorter alignments will be excluded (1 to 1e+6, default: off) - **--qcfilter** \ Query coverage filter for BLAST hits. Hits with less coverage will be excluded (0 to 100, default: off) - **--ifilter** \ Identity filter for BLAST hits. Hits with less identity will be excluded (0 to 100, default: off) - **--evfilter** \ E-value filter for BLAST hits. Hits with larger e-values will be excluded (1e-999 to 9.9e1, default: off) - **--bsfilter** \ Bit score filter for BLAST hits. Hits with lower bit scores will be excluded (0 to 1e+6, default: off) **BLAST query paths** These settings control how Bandage searches for query paths after conducting a BLAST search. - **--pathnodes** \ The number of allowed nodes in a BLAST query path (1 to 50, default: 6) - **--minpatcov** \ Minimum fraction of a BLAST query which must be covered by a query path (0.3 to 1, default: 0.9) - **--minhitcov** \ Minimum fraction of a BLAST query which must be covered by BLAST hits in a query path (0.3 to 1, default: 0.9) - **--minmeanid** \ Minimum mean identity of BLAST hits in a query path (0 to 1, default: 0.5) - **--maxevprod** \ Maximum e-value product for all BLAST hits in a query path (1e-999 to 9.9e1, default: 1e-10) - **--minpatlen** \ Minimum allowed relative path length as compared to the query (0 to 10000, default: 0.95) - **--maxpatlen** \ Maximum allowed relative path length as compared to the query (0 to 10000, default: 1.05) - **--minlendis** \ Minimum allowed length discrepancy (in bases) between a BLAST query and its path in the graph (**-1e**+6 to 1e+6, default: off) - **--maxlendis** \ Maximum allowed length discrepancy (in bases) between a BLAST query and its path in the graph (**-1e**+6 to 1e+6, default: off) ## SEE ALSO Online Bandage help: https://github.com/rrwick/Bandage/wiki ## AUTHOR This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.