diff --git a/README.md b/README.md
index a0c56b5..c9346ee 100644
--- a/README.md
+++ b/README.md
@@ -1,17 +1,49 @@
+[](https://travis-ci.org/lh3/minigraph)
+[](https://lh3.github.io/minigraph/)
+[](https://anaconda.org/bioconda/minigraph)
+[
](https://quay.io/repository/biocontainers/minigraph)
+[
](https://quay.io/repository/biocontainers/minigraph)
+[](https://anaconda.org/bioconda/minigraph)
+
+minigraph
+=========================================
+
+Seq-to-graph mapper and graph generator
+
+## Table of Contents
+
+
+
+- [Getting Started](#started)
+- [Introduction](#intro)
+- [Users' Guide](#uguide)
+ - [Installation](#install)
+ - [Sequence-to-graph mapping](#map)
+ - [Graph generation](#ggen)
+ - [Calling structural variations](#callsv)
+ - [SV calling showcase (human MHC)](#svexample)
+ - [Prebuilt graphs](#prebuilt)
+ - [Algorithm overview](#algo)
+- [Limitations](#limit)
+
## Getting Started
```sh
-git clone https://github.com/lh3/minigraph
-cd minigraph && make
# Map sequence to sequence, similar to minimap2 without base alignment
./minigraph test/MT-human.fa test/MT-orangA.fa > out.paf
+
# Map sequence to graph
./minigraph test/MT.gfa test/MT-orangA.fa > out.gaf
+
# Incremental graph generation (-l10k necessary for this toy example)
./minigraph -cxggs -l10k test/MT.gfa test/MT-chimp.fa test/MT-orangA.fa > out.gfa
+
# Call per-sample path in each bubble/variation (-c not needed for this)
./minigraph -xasm -l10k --call test/MT.gfa test/MT-orangA.fa > orangA.call.bed
+# The lossy FASTA representation (requring https://github.com/lh3/gfatools)
+gfatools gfa2fa -s out.gfa > out.fa
+
# Extract localized structural variations
gfatools bubble out.gfa > SV.bed
@@ -20,22 +52,6 @@ curl -sL https://zenodo.org/record/8245267/files/mg-cookbook-v1_x64-linux.tar.bz
cd mg-cookbook-v1_x64-linux && ./00run.sh
```
-## Table of Contents
-
-
-
-- [Getting Started](#started)
-- [Introduction](#intro)
-- [Users' Guide](#uguide)
- - [Installation](#install)
- - [Sequence-to-graph mapping](#map)
- - [Graph generation](#ggen)
- - [Calling structural variations](#callsv)
- - [SV calling showcase (human MHC)](#svexample)
- - [Prebuilt graphs](#prebuilt)
- - [Algorithm overview](#algo)
-- [Limitations](#limit)
-
## Introduction
Minigraph is a sequence-to-graph mapper and graph constructor. For graph
@@ -57,6 +73,10 @@ To install minigraph, type `make` in the source code directory. The only
non-standard dependency is [zlib][zlib]. For better performance, it is
recommended to compile with recent compliers.
+```sh
+git clone https://github.com/lh3/minigraph
+cd minigraph && make
+```
### Sequence-to-graph mapping
To map sequences against a graph, you should prepare the graph in the [GFA