- Necessary updates to keep up with changes in TBB
- Updated the readme: added more detailed clarification for the parameter -a (vertex frequency threshold)
- Made GFF output compliant with the GFF3 specification
- Added a pragma to GFF output showing the lengths of input sequences
- Fixed the incorrect path to spoa in bioconda version
- Reduced the number of temporary files created during the global alignment phase
- Removed dependency on GNU time from the main SibeliaZ script
- Updated the version of spoa
- Added submodule maf2synteny, a program for constructing synteny blocks from the output of Sibeliaz
- Fixed a bug in SibeliaZ script resulting in failed global alignment calls in certain cases
- Updated the version of TwoPaCo
- Fixed a bug resulting in missing of some collinear blocks
- Added script "glue_gfa1.py" that glues back GFA1 produced by "maf_to_gfa1.py" to the original genomes
- Fixed inconsistent use of spaces and tabs in "maf_to_gfa1.py"
- MAF file now contains the version number and the arguments used
- The results are now deterministic and do not depend on the number of threads
- Changed behavior of "-f" flag: now it is optional and only controls size of the Bloom filter allocated by TwoPaCo. By default, it is now thrice of the total input file size
- Fixed a bug in handling corrupt FASTA files
- Slightly improved accuracy
- Added a script to convert MAF alignment to XMFA (maf_to_xmfa.py)
- Added a script for converting MAF alignment to GFA1 (maf_to_gf1.py)
- Input genomes can be provided in multiple FASTA files now
- Fixed a bug causing some blocks to overlap by k basepairs
- Fixed a bug resulting some exact matching blocks to be missing
- Hello, World!