Merge pull request #594 from Overcraft90/patch-1

Update README.md [skip ci]

README.md

@@ -120,6 +120,31 @@ docker run odgi
 An alternative way to manage `odgi`'s dependencies is by using the `GNU GUIX` package manager. We use Guix to develop, test and deploy odgi on our systems.
 For more information see [INSTALL](./INSTALL.md).
 
+## FAQs
+
+`odgi` is supported by default by [`PGGB`](https://github.com/pangenome/pggb). However, it cannot be run out-of-the-box with [`minigraph-CACTUS`](https://github.com/ComparativeGenomicsToolkit/cactus/blob/master/doc/pangenome.md) pangenomes; this requires few steps for the conversion from GFA v1.1 to GFA v1.0 — which is the one used by `odgi`. The main difference between the two is whether or not including a W field to encode walks in the pangenome graph, a feature that is not as yet supported in `odgi`; hence why `minigraph-CACTUS` has to go through the following conversion step:
+
+```
+vg convert -W -t <n_of_threads> -g <pangenome_v1.1>.gfa -f > <pangenome_v1.0>.gfa
+```
+
+After converting the `minigraph-CACTUS` graph in GFA v1.0 format; it is then possible to do all conventional `odgi` analyses. For instance:
+
+```
+odgi build -g <pangenome_v1.0>.gfa -o <graph>.og -s -O -t <n_of_threads>
+```
+
+which is often useful to speed up `odgi` operations using its native format, especially when integrated into pipelines or called multiple times. Afterwards, paths can be extracted with `odgi paths`
+
+```
+odgi paths -i <graph.og> -L -t <n_of_threads> | cut -f 1,2 -d '#' | sort | uniq > <prefixes>.tsv
+```
+
+and, lasty, any 1D visualization or 2D layout can be produced also for this graph. Below, an example of a 1D viz that colors haplotypes based on their ID:
+
+```
+odgi viz -i <graph>.og -o <graph_viz>.png -s # -M <prefixes>.tsv -t <n_of_threads>
+```
 
 ## documentation