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Re-arrange Readme #97

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add badges in readme
Juke34 Jun 7, 2023
c1e1c27
Update README.md
Juke34 Jun 7, 2023
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51 changes: 34 additions & 17 deletions README.md
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Original file line number Diff line number Diff line change
@@ -1,23 +1,14 @@
[![Build Status](https://travis-ci.org/lh3/minigraph.svg?branch=master)](https://travis-ci.org/lh3/minigraph)
## <a name="started"></a>Getting Started
[![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)

```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
minigraph
=========================================

# 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
```
Seq-to-graph mapper and graph generator

## Table of Contents

Expand All @@ -34,6 +25,28 @@ gfatools bubble out.gfa > SV.bed
- [Algorithm overview](#algo)
- [Limitations](#limit)

## <a name="started"></a>Getting Started

```sh
# 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
```

## <a name="intro"></a>Introduction

Minigraph is a sequence-to-graph mapper and graph constructor. For graph
Expand All @@ -55,6 +68,10 @@ 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
Expand Down