1.0.0

This release introduces several significant updates, including a complete rewrite of the algorithm in Rust to boost both speed and reliability in graph construction. PanGraph can now be compiled as a standalone binary, greatly simplifying installation. The release also contains several breaking changes.

Major changes

• Graph Construction Algorithm Enhancements

  • Block merging has been refined and simplified: when merging two blocks, sequences are re-aligned to the block consensus, resulting in more robust alignments.
  • The alignment process is now easily parallelizable, extending beyond the previous limitation of parallel guide tree traversal.
  • Insertions are now placed on the consensus sequence without aligning them to each other, simplifying bookkeeping of alignment variation when merging blocks.

• Graph JSON Output Format Updates

  • A new nodes dictionary links paths and blocks.
  • Entries in the paths dictionary have been simplified to include only lists of nodes.
  • Block alignments now use a simpler encoding; insertions are placed on the consensus without alignment, eliminating the need for a separate gaps entry.

• Command Line Interface Modifications

  • Improved parallelization control with the new --jobs flag.
  • The export command has been restructured into several subcommands:
    • export gfa – Export the graph in GFA format.
    • export block-consensus – Export block consensus sequences in a single FASTA file.
    • export block-sequences – Export each block’s alignment in separate FASTA files.
    • export core-genome – Export the core-genome alignment.
  • The marginalize command has been renamed to simplify.
  • A new reconstruct command has been added to rebuild the input sequences from the graph.
  • The polish and generate commands have been removed.

Installation and usage 📚 Documentation: docs.pangraph.org 📥 Standalone native executables: download using links in the "Assets" section just below 🐋 Docker images: neherlab/pangraph