ntJoin v1.0.4

• Release version v1.0.4
• Performance improvements for computing minimizers (indexlr)
• Time logging per step is now optional (turn on with time=True)
• Bugfixes

ntJoin v1.0.3

• Release version v1.0.3
• Added max gap size parameter (G)
• Fix edge case that could cause duplicated sequence in output scaffolds
• Strip terminal Ns from unassigned scaffolds

ntJoin v1.0.2

• Release version v1.0.2
• Added option to not make any cuts in the input contigs (no_cut=True)
• Added option to output scaffold layouts in agp format (agp=True)
• Included small test example for testing installation
• Can now handle input fasta files with any file extension
• Bug fixes

ntJoin v1.0.1

• Release version v1.0.1
• indexlr now uses 2 hash functions to avoid bias
  • First hash value used to select the minimum in the window
  • Second hash value used for sketch
• Use single process by default for ntjoin_assemble.py (parameter assemble_t in ntJoin)

ntJoin v1.0.0

Initial release of ntJoin: Scaffolding assemblies using reference assemblies and minimizer graphs