diff --git a/README.md b/README.md index a0c56b5..c9346ee 100644 --- a/README.md +++ b/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) +[docker_minigrapht](https://quay.io/repository/biocontainers/minigraph) +[singularity_minigraph](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 + + + +- [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