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DOC: some readme tweaking
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fedarko committed Jan 3, 2024
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Expand Up @@ -213,13 +213,14 @@ and **two edges** (`1 -> 2`, `-2 -> -1`). The presence of node `X`
["implies"](https://github.com/bcgsc/abyss/wiki/ABySS-File-Formats#reverse-complement)
the existence of the reverse complement node `-X`, and the presence of edge
`X -> Y` "implies" the existence of the reverse complement edge `-Y -> -X`.
This is analogous to [how "double mode" works in Bandage](https://github.com/rrwick/Bandage/wiki/Single-vs-double-node-style).
Interpreting the graph file in this way is analogous to
[how "double mode" works in Bandage](https://github.com/rrwick/Bandage/wiki/Single-vs-double-node-style).

#### Impacts of reverse complement nodes / edges on the graph structure

Often, the presence of reverse complement nodes / edges (whether
they are explicitly described in a FASTG, DOT, or GML file, or are implicitly
described in a GFA or LastGraph file) doesn't impact the graph structure much.
described in a GFA or LastGraph file) **doesn't impact the graph structure much**.

What does this mean? Consider the GFA example above. There are four nodes and
two edges in this graph, but they form two
Expand Down Expand Up @@ -275,7 +276,7 @@ for details on how we handle reverse complements in FASTG files.)
<details>
<summary><strong>What happens if an edge is its own reverse complement?</strong></summary>

You really like asking hard questions, don't you? ;)
You really like asking hard questions, don't you?

This can happen if an edge exists from `X -> -X` or from `-X -> X` in an
"implicit" graph file (GFA / LastGraph). Consider
Expand Down Expand Up @@ -320,10 +321,10 @@ then that's also fine.)
Yes! MetagenomeScope now supports
[multigraphs](https://en.wikipedia.org/wiki/Multigraph). If your assembly graph
file describes more than one edge from `X -> Y`, then MetagenomeScope will
visualize all of these "parallel" edges. (This situation often occurs when
visualizing de Bruijn graphs stored in DOT files.)
visualize all of these "parallel" edges. (Parallel edges often occur in de
Bruijn graphs.)

Notably, this is only supported right now for some filetypes. The
Notably, parallel edges are only supported right now for some filetypes. The
parsers MetagenomeScope uses for GFA and FASTG files
[do not allow multigraphs](https://github.com/marbl/MetagenomeScope/issues/239) -- this
means that, at the moment, trying to use MetagenomeScope to visualize a GFA or
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