Welcome to the PGGB world!

In standard genomic approaches sequences are related to a single linear reference genome introducing reference bias. Pangenome graphs encoded in the variation graph data model describe the all versus all alignment of many sequences.

pggb renders a collection of sequences into a pangenome graph, in the variation graph model. Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining local linearity is important for the interpretation, visualization, and reuse of pangenome variation graphs.

Core packages

wfmash

Pairwise sequence alignment with wfmash

seqwish

Graph induction with seqwish

  • Build alignment graph with interval tress

  • Compute transitive closure of bases

  • Path tracing yields variation graph

  • Raw pangenome graph in GFAv1 format

smoothxg

Graph normalization with smoothxg

  • Global graph sorting with PG-SGD

  • Break graph into blocks

  • Smooth blocks via POA

  • Graph has partial local order

  • Smoothed graph in GFAv1 format

Contributed packages

Moreover, the pipeline supports identification and collapse of redundant structure with GFAffix. Optional post-processing steps with ODGI provide 1D and 2D diagnostic visualizations of the graph and basic graph metrics. Variant calling is also possible with vg deconstruct to obtain a VCF file relative to any set of reference sequences used in the construction. It utilizes a path jaccard concept to correctly localize variants in segmental duplications and variable number tandem repeats. In the HPRC data, this greatly improved variant calling performance.

The output graph (*.smooth.fix.gfa) is suitable for read mapping in vg or with GraphAligner.

A Nextflow version of pggb is currently developed on nf-core/pangenome. This pipeline presents an implementation that scales better on a cluster.

Pipeline Workflow

_images/pggb-flow-diagram.png

Citation

IN PREPARATION

Core Functionalities

Click on the images below for more details.

tutorial_one

Tutorial one

  • Step 1

  • Step 2

  • Step 3

Index