Bandage - Bioinformatics Application for Navigating De novo
Assembly Graphs Easily
Bandage <command> [options]
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..
- <blank> 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
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
<scope>
- Graph scope, from one of the following options: entire, aroundnodes,
aroundblast, depthrange (default: entire)
- --nodes
<list>
- 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
<int>
- The number of node steps away to draw for the aroundnodes and aroundblast
scopes (0 to 100, default: 0)
- --mindepth
<float>
- The minimum allowed depth for the depthrange scope (0 to 1e+6, default:
10)
- --maxdepth
<float>
- 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
<float>
- Node length per megabase (0 to 1e+6, default: auto)
- --minnodlen
<float>
- Minimum node length (1 to 100, default: 5)
- --edgelen
<float>
- Edge length (0.1 to 100, default: 5)
- --edgewidth
<float>
- Edge width (0.1 to 100, default: 1.5)
- --doubsep
<float>
- Double mode separation (0 to 100, default: 2)
Graph layout
- --nodseglen
<float>
- Node segment length (1 to 1000, default: 20)
- --iter
<int>
- Graph layout iterations (0 to 4, default: 2)
- --linear
- Linear graph layout (default: off)
Graph appearance
- --edgecol
<col>
- Colour for edges (default: black)
- --outcol
<col
- Colour for node outlines (default: black)
- --outline
<float>
- Node outline thickness (0 to 100, default: 0)
- --selcol
<col>
- 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
<col>
- Colour for label text (default: black)
- --toutcol
<col>
- Colour for text outline (default: white)
- --toutline
<float>
- 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
<float>
- Average node width (0.5 to 1000, default: 5)
- --depwidth
<float>
- Depth effect on width (0 to 1, default: 0.5)
- --deppower
<float>
- 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
<int>
- Font size for node labels (1 to 100, default: 12)
Node colours
- --colour
<scheme>
- 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
<int>
- Positive node saturation (0 to 255, default: 127)
- --ransatneg
<int>
- Negative node saturation (0 to 255, default: 127)
- --ranligpos
<int>
- Positive node lightness (0 to 255, default: 150)
- --ranligneg
<int>
- Negative node lightness (0 to 255, default: 90)
- --ranopapos
<int>
- Positive node opacity (0 to 255, default: 255)
- --ranopaneg
<int>
- Negative node opacity (0 to 255, default: 255)
Uniform colour scheme
These settings only apply when the uniform colour scheme is
used.
- --unicolpos
<col>
- Positive node colour (default: firebrick)
- --unicolneg
<col>
- Negative node colour (default: maroon)
- --unicolspe
<col>
- Special node colour (default: green)
Depth colour scheme
These settings only apply when the depth colour scheme is
used.
- --depcollow
<col>
- Colour for nodes with depth below the low depth value (default:
black)
- --depcolhi
<col>
- Colour for nodes with depth above the high depth value (default: red)
- --depvallow
<float>
- Low depth value (0 to 1e+6, default: auto)
- --depvalhi
<float>
- High depth value (0 to 1e+6, default: auto)
BLAST search
- --query
<fastafile>
- A FASTA file of either nucleotide or protein sequences to be used as BLAST
queries (default: none)
- --blastp
<param>
- 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
<int>
- Alignment length filter for BLAST hits. Hits with shorter alignments will
be excluded (1 to 1e+6, default: off)
- --qcfilter
<float>
- Query coverage filter for BLAST hits. Hits with less coverage will be
excluded (0 to 100, default: off)
- --ifilter
<float>
- Identity filter for BLAST hits. Hits with less identity will be excluded
(0 to 100, default: off)
- --evfilter
<sci>
- E-value filter for BLAST hits. Hits with larger e-values will be excluded
(1e-999 to 9.9e1, default: off)
- --bsfilter
<float>
- 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
<int>
- The number of allowed nodes in a BLAST query path (1 to 50, default:
6)
- --minpatcov
<float>
- Minimum fraction of a BLAST query which must be covered by a query path
(0.3 to 1, default: 0.9)
- --minhitcov
<float>
- 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
<float>
- Minimum mean identity of BLAST hits in a query path (0 to 1, default:
0.5)
- --maxevprod
<sci>
- Maximum e-value product for all BLAST hits in a query path (1e-999 to
9.9e1, default: 1e-10)
- --minpatlen
<float>
- Minimum allowed relative path length as compared to the query (0 to 10000,
default: 0.95)
- --maxpatlen
<float>
- Maximum allowed relative path length as compared to the query (0 to 10000,
default: 1.05)
- --minlendis
<int>
- Minimum allowed length discrepancy (in bases) between a BLAST query and
its path in the graph (-1e+6 to 1e+6, default: off)
- --maxlendis
<int>
- Maximum allowed length discrepancy (in bases) between a BLAST query and
its path in the graph (-1e+6 to 1e+6, default: off)
Online Bandage help: https://github.com/rrwick/Bandage/wiki
This manpage was written by Andreas Tille for the Debian
distribution and can be used for any other usage of the program.