ntJoin v1.1.5

• Release version 1.1.5
• Fix for cases where no scaffolding was seen for circular references (#113)
  • With fix, circular graphs are detected and properly used for scaffolding sequences
• Documentation update - ensure that any terminal N's in sequences are removed prior to ntJoin

ntJoin v1.1.4

• Release version v1.1.4
• Large code refactor
• Bugfixes

ntJoin v1.1.3

• Release version v1.1.3
• Bugfix for edge case
  • Where there are no paths found and overlap=True

ntJoin v1.1.2

• Release version v1.1.2
• Fix for compatibility with new pybedtools version (v0.9.1+)
• Code refactoring
• Documentation updates

ntJoin v1.1.1

• Release version v1.1.1
• Make btllib a dependency (removed packaged btllib)
• Documentation updates

ntJoin v1.1.0

• Release version v1.1.0
• Introduces new 'overlap' feature, which is enabled by default (overlap=True)
  • For adjacent sequences that have a putative overlap based on gap distance estimates:
    • Compute minimizers with a lower k and w (to increase sensitivity), and create an undirected minimizer graph using minimizers found in the putative overlap region (in multiplicity of 1 in both sequences)
    • Use the minimizer graph to anchor the sequences to each other, and use the coordinates to trim the overlapping sequence
  • This feature reduces the incidence of local misassemblies and duplications, created when overlapping sequences are naively joined end-to-end
• Update btllib to v1.4.4
• General bugfixes and documentation updates

ntJoin v1.0.8

• Release version v1.0.8
• Add support for multi-line fasta files
• Update btllib dependency to v1.1.5

ntJoin v1.0.7

• Release version v1.0.7
• Update btllib dependency (to v1.1.2)
• Bugfixes

ntJoin v1.0.6

• Release version v1.0.6
• Added optional parameter reference_config, which can be used to specify a config file that lists the reference(s) and reference_weight(s)
  • Previous ntJoin usage will work in exactly the same way if this parameter is not used - this feature is just provided for convenience, particularly for specifying multiple references
  • Config file expected to be in csv format in the form:

reference_1.fa,reference_weight_1
reference_2.fa,reference_weight_2

ntJoin v1.0.5

• Release version v1.0.5
• Fixes for indexlr