BANDAGE(1)

📦 version 0.9.0, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

✨ BANDAGE(1) ✨ User Commands 💖

Okay bestie, gather around 🫶 This is the manual page for Bandage, and the manual name is Bandage - Bioinformatics Application for Navigating De novo Assembly Graphs Easily 🦋. Yes, that's a whole mouthful, but it's giving exactly what it promises.

🌸 NAME 🌸

Bandage — Bioinformatics Application for Navigating De novo Assembly Graphs Easily 💅

🧚 SYNOPSIS 🧚

Bandage <command> [options]

💜 DESCRIPTION 💜

Okay so Bandage is a GUI program that lets you poke around the assembly graphs made by de novo assemblers like Velvet, SPAdes, MEGAHIT and others. Literally iconic 😭🔥

👑 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 🎨

Bestie, these options configure the Bandage settings you can also find in the Bandage GUI. It's giving customization queen ✨

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). Don't skip this, it's a whole vibe check 💀

🌟 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, picked from entire, aroundnodes, aroundblast, or 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, no cap it's a little math-y but you got this 🧮

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, picked from random, uniform, depth, blastsolid, or blastrainbow (default: random if --query isn't used, blastsolid if --query is 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) 🔼
  • --query <fastafile> — A FASTA file of either nucleotide or protein sequences to use as BLAST queries (default: none) 🧬
  • --blastp <param> — Parameters to be used by blastn and tblastn when running a BLAST search in Bandage (default: none). Format BLAST parameters exactly as you'd use them for blastn/tblastn on the command line, and wrap them in quotes 🎀
  • --alfilter <int> — Alignment length filter for BLAST hits. Hits with shorter alignments get excluded (1 to 1e+6, default: off) ✂️
  • --qcfilter <float> — Query coverage filter for BLAST hits. Hits with less coverage get excluded (0 to 100, default: off) 📉
  • --ifilter <float> — Identity filter for BLAST hits. Hits with less identity get excluded (0 to 100, default: off) 🪞
  • --evfilter <sci> — E-value filter for BLAST hits. Hits with larger e-values get excluded (1e-999 to 9.9e1, default: off) 🧪
  • --bsfilter <float> — Bit score filter for BLAST hits. Hits with lower bit scores get excluded (0 to 1e+6, default: off) 🎯

🛤️ BLAST query paths 🛤️

These settings control how Bandage hunts for query paths after running 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 that must be covered by a query path (0.3 to 1, default: 0.9) 📏
  • --minhitcov <float> — Minimum fraction of a BLAST query that 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 compared to the query (0 to 10000, default: 0.95) 📉
  • --maxpatlen <float> — Maximum allowed relative path length 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. Huge thanks to Andreas for the rewrite 🫶

Bandage 0.8.1, August 2018, BANDAGE(1) — go forth and graph responsibly, bestie 💖🦋✨

📦 where this page comes from