ntLink v1.3.1

• Release v1.3.1
• Fixed bug that could lead to a file name collision at the gap-filling stage when running parameter sweeps in the same directory
• Changed PYTHONPATH assignment in ntLink makefile to append to existing PYTHONPATH environment variable, not overwrite it
• Documentation updates

ntLink v1.3.0

• Release v1.3.0
• Added code to allow for in-code liftover-driven rounds of ntLink
  • More scaffolding gains can be achieved by running additional rounds of ntLink scaffolding
  • This is powered by the ntLink_rounds makefile and ntlink_liftover_mappings.py, which lifts over the mapping coordinates to the post-ntLink assembly for a given round
• Fix to ensure that rounds of ntLink run deterministically
• Bugfix to verbose mapping file output
• Documentation updates
• General bugfixes

ntLink v1.2.1

• Release v1.2.1
• Update btllib to v1.4.4
  • Fixes issue with compiling btllib using python 3.8

ntLink v1.2.0

• Release v1.2.0
• Introduce new gap-filling feature
  • If the target gap_fill is specified, ntLink will attempt to fill the ntLink-derived scaffold gaps using information about which reads supported the given sequence join
  • Currently, the read with the highest average mapping minimizers is chosen, and sequence from the read used to fill in the gap
• Update btllib dependency to v1.4.3
• Bugfixes

ntLink v1.1.3

• Release v1.1.3
• Update btllib dependency to v1.3.0
  • With new btllib version (compiled static library), update compilation for indexlr

ntLink v1.1.2

• Release v1.1.2
• Fix for naming scaffolds in iterative ntLink runs
  • With iterative runs, could see failures due to duplicate headers
  • Detects if scaffolds are present with ntLink_<number> convention
  • If so, increments number for output scaffolds accordingly
• Update btllib dependency to v1.1.9

ntLink v1.1.1

• Release v1.1.1
• Bugfix for rare edge case where adjacent contigs in a path do not have a direct edge in the scaffold graph (overlap stage)
• Adjust targets in ntLink to avoid re-doing unnecessary steps if re-launching ntLink

ntLink v1.1.0

• Release v1.1.0
• Add new feature overlap (defaults to True)
  • If overlap=True, ntLink will attempt to detect when contigs being joined overlap, and trim them to avoid duplicating sequence
  • Trimming reduces misassemblies by avoiding the introduction of insertions in locations where contigs being joined overlap
  • More details in the ntLink wiki: https://github.com/bcgsc/ntLink/wiki/Overlap-Feature
• Add support for multi-line fasta and fastq files
• Update btllib dependency to v1.1.6
• Change default prefix to <target>.k<k>.w<w>.n<n>
• Update documentation and CI tests

ntLink v1.0.1

• Release v1.0.1
• Update btllib (to v1.1.2)
• Update demo tests
• Improve documentation and log messages
• Bugfixes

ntLink v1.0.0

Initial release of ntLink: Genome scaffolding using long reads and minimizers