NPG-explorer 0.4.0 released

12 Jun 2015

NPG-explorer is a new tool for nucleotide pangenome construction and analysis of closely related prokaryotic genomes.

Version 0.4.0 was released on Jun 12, 2015.

This release has a focus on new developments and a few bug fixes.

Changes:

Change alignment requirements. Require high similarity in every slice of length MIN_LENGTH. Use logarithmic gap penalty. Introduce option MIN_END. Do not require length of fragment >= MIN_LENGTH.
Short blocks of one fragment are now called minor blocks. All minor blocks are shorter than MIN_LENGTH.
GUI/BSA: show block’s length for global blocks.
Use Travis CI: https://travis-ci.org/npge/npge
BlockSet alignment: g-blocks and i-blocks. G-blocks are formed from joined consequent s-blocks. S-blocks are always aligned in g-blocks. Other blocks form i-blocks.
Speed up SplitRepeats. Improve time complexity by building the tree from diagnostic positions. Critical for blocks of > 500 fragments.
PostProcessing produces new files:
- table of global blocks’ properties (*.gbi)
- blockset alignments with block names (*.blocks)
- pangenome-small.bi
- nj-global-tree-full.tre
- genes/partition.tsv
Mutations file parser written in Python (example)
Print local time with timezone offset to logs
Add descriptions of some algorithms (*.md files)
Translate ECCB’14 abstract into Russian
Fix bugs:
- Fix bugs in GUI
- Fix bugs in annotations parser (GetData)
- Fix bugs in local blockset alignment builder. It used to consider linear sequences to be circular.

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