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NEWS.md

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Sibelia 3.0.7

  • Fixed a compilation error for newer versions of GCC

Sibelia 3.0.6

  • Fixed a bug with crash when 0 simplificaiont stages specified
  • When both --graphfile" and --visualize are set, graph is output at each stage
  • Added commandline option --noblocks

Sibelia 3.0.5

  • Removed commandline options: -a, --alignment
  • Added commandline options: --maf
  • Added the third parameters set "far"
  • Changed permissions of LAGAN scripts to run on some platforms
  • Changed structure of the directory "share" (Linux platforms only)
  • Fixed a bug with misorder of aligned repeats (affected -a option of C-Sibelia only)
  • Fixed some compiler warnings yielded by LAGAN sources
  • Fixed a bug in hierarchy circos output that resulted in uncompilable configs for some datasets

Sibelia 3.0.4

  • Released postprocessing scripts for circos pictures (see CIRCOS_HELPER.md)
  • Fixed a few bugs caused by large amount of 'N' characters in the input
  • Fixed crash of C-Sibelia with large block size threshold

Sibelia 3.0.3

  • Updated snpEff to version 3.3f
  • C-Sibelia now produces alignments of repeats within genomes

Sibelia 3.0.2

  • Fixed a bug in FASTA parser caused by Windows line endings on Unix-like systems

Sibelia 3.0.1

  • Fixed a bug in C-Sibelia: incorrect reporting of variants within synteny blocks having opposite directions
  • Added output of synteny blocks in GFF format
  • Removed sequences without synteny blocks from Circos diagrams
  • Blocks orientations are depicted on Circos diagram by different colors
  • Added Sibelia cmd options: --nopostprocess, --allstages, --correctboundaries, --gff, --lastk
  • Added C-Sibelia cmd options: -o, -a
  • C-Sibelia outputs whole genome alignments in XMFA format (-o flag)
  • Slightly changed "fine" parameters simplification set

Sibelia 3.0.0

  • C-Sibelia is functional now
  • Variant annotation with snpEff
  • Directory structure on Unix system is more conventional

Sibelia 2.1.2

  • Fixed crashes on some input genomes

Sibelia 2.1.1

  • Got rid of overlap between synteny blocks, overlapping regions are granted to the blocks with higher multiplicity
  • Added generation of circos picture that shows blocks at multiple stages simultaneously
  • Added cmd option: -v

Sibelia 2.1.0

  • Improved performance in the case of many genomes. Now it is possible to compute synteny blocks for 59 E.coli genomes within 70 minutes and 8 GB of RAM on a standard desktop
  • Synteny block boundaries now are more precise

Sibelia 2.0.1

  • Improved diagram appearance
  • Fixed bug with multiple input files
  • Fixed circos generation in case of many input sequencs
  • Changed format of coordinates of synteny blocks, see USAGE.md, section "Blocks coordinates"

Sibelia 2.0.0

  • Improved performance
  • Completed manual
  • Added d3 visualization
  • Removed cmd options: -c -p -d
  • Changed behaviour of the options: -q -g -r
  • Added cmd options: -t -o

Sibelia 1.0.0

  • Initial release