Provided by: bandage_0.8.1-1_amd64 bug

NAME

       Bandage - Bioinformatics Application for Navigating De novo Assembly Graphs Easily

SYNOPSIS

       Bandage <command> [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
       <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

   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 <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)

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.