minigraph for Mac

Getting Started

Getting Started Introduction Users' Guide Installation Sequence-to-graph mapping Graph generation Calling structural variations SV calling showcase (human MHC) Prebuilt graphs Algorithm overview Limitations

Introduction

Minigraph is a sequence-to-graph mapper and graph constructor. For graph generation, it aligns a query sequence against a sequence graph and incrementally augments an existing graph with long query subsequences diverged from the graph. The figure on the right briefly explains the procedure.

Minigraph borrows ideas and code from minimap2. It is fairly efficient and can construct a graph from 90 human assemblies in a couple of days using 24 CPU cores. Older versions of minigraph was unable to produce base alignment. The latest version can. Please add option -c for graph generation as it generally improves the quality of graphs.

Users' Guide

Installation

To install minigraph, type make in the source code directory. The only non-standard dependency is zlib. For better performance, it is recommended to compile with recent compliers.

Sequence-to-graph mapping

To map sequences against a graph, you should prepare the graph in the GFA format, or preferrably the rGFA format. If you don't have a graph, you can generate a graph from multiple samples (see the Graph generation section below). The typical command line for mapping is

You may choose the right preset option -x according to input. Minigraph output mappings in the GAF format, which is a strict superset of the PAF format. The only visual difference between GAF and PAF is that the 6th column in GAF may encode a graph path like MT_human:0-4001Graph generation

The following command-line generates a graph in rGFA:

which is equivalent to

File ref.fa is typically the reference genome (e.g. GRCh38 for human). It can also be replaced by a graph in rGFA. Minigraph assumes sample1.fa to be the whole-genome assembly of an individual. This is an important assumption: minigraph only considers 1-to-1 orthogonal regions between the graph and the individual FASTA. If you use raw reads or put multiple individual genomes in one file, minigraph will filter out most alignments as they cover the input graph multiple times.

The output rGFA can be converted to a FASTA file with gfatools:

The output out.stable.fa will always include the initial reference ref.fa and may additionally add new segments diverged from the initial reference.

Calling structural variations

A minigraph graph is composed of chains of bubbles with the reference as the backbone. Each bubble represents a structural variation. It can be multi-allelic if there are multiple paths through the bubble. You can extract these bubbles with

The output is a BED-like file. The first three columns give the position of a bubble/variation and the rest of columns are:

(4) # GFA segments in the bubble including the source and the sink of the bubble