KAnalyze / Blog: Recent posts

• Large k-mers
  • Tested up to 3000-mer
• Removed GUI from count module
• Default output format is auto
  • Was raw
  • --input is raw if -f is auto
• Output format "int" is gone
  • Use "dec"
• New output format: IKC (indexed k-mer count)
  • Query k-mers in sequence order almost as fast as loading into memory
  • Requires a minimizer to be set.
• Reverse-complement "duplicate" does not count self-complementary k-mers
  • Use "forceduplicate" for old behavior
• Minimizers
  • -m ikc
  • --minsize > 0 required
• FASTA format writer: No space after ">"
• Command-line options
  • -t: Changed from --temploc to --threads
  • -g (--segsize) can accept decimal values (e.g. 1.5G)

KAnalyze 0.9.7 has been released!

The new version fixes a discrepency for the output formats "DEC" and "INT" for k-mers in decimal-integer format. The help and documentation use "DEC", but for those using "INT", it is now an alias.

Both the count and stream modules have a "-m" (--outfmt) option to set the output type. The count GUI also now has a format field.

If you were using the "countgui" scripts packaged with the Windows or Linux distribution, please use the "count" script. When launched with no command line arguments, the count module automatically goes into GUI mode.... read more