Re-arrange Readme

README.md

@@ -1,17 +1,49 @@
+[![Build Status](https://travis-ci.org/lh3/minigraph.svg?branch=master)](https://travis-ci.org/lh3/minigraph)
+[![Documentation Status](https://img.shields.io/badge/doc-passing-brightgreen)](https://lh3.github.io/minigraph/)
+[![BioConda Install](https://img.shields.io/conda/dn/bioconda/minigraph.svg?style=flag&label=BioConda%20install)](https://anaconda.org/bioconda/minigraph)
+[<img alt="docker_minigrapht" src="https://img.shields.io/badge/container-Docker-blue">](https://quay.io/repository/biocontainers/minigraph)
+[<img alt="singularity_minigraph" src="https://img.shields.io/badge/container-Singularity-orange">](https://quay.io/repository/biocontainers/minigraph)
+[![Anaconda-Server Badge](https://anaconda.org/bioconda/minigraph/badges/license.svg)](https://anaconda.org/bioconda/minigraph)
+
+minigraph
+=========================================
+
+Seq-to-graph mapper and graph generator
+
+## Table of Contents
+
+<img align="right" width="278" src="doc/example1.png"/>
+
+- [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)
+
 ## <a name="started"></a>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
-
-<img align="right" width="278" src="doc/example1.png"/>
-
-- [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)
-
 ## <a name="intro"></a>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
+```
 ### <a name="map"></a>Sequence-to-graph mapping
 
 To map sequences against a graph, you should prepare the graph in the [GFA