v2.2.2 was fine except that -O3 flag was deactivated, hence BCALM was slower than it needed. This release fixes that.

No new features, just a collection of the bugfixes applied since last year. Should be the most stable bcalm version ever

Just a bugfix release

• Perfectly circular unitigs are now output, instead of being discarded with a warning.
• Fixed a multi-threading bug (#37) that caused invalid links on some systems.

• GFA output using a python script, see README.
• Speed and memory improvements.
• This release is also a bugfix release: previous version had a small number of wrong compactions as well as wrong edges between unitigs (multi-threading bug, and palindromic k-1-mers bug).

Thanks to Marco Previtali, Mikko Rautiainen, Guillaume Holley, Fatemeh Almodaresi, Vincenzo Bonnici, for reporting bugs.

• Arbitrary large kmer lengths
• Reporting mean k-mer abundance of unitigs
• Edge are reported in the FASTA header of unitigs

BCALM v2.0.0

This version, modulo some small tweaks and bugfixes (commits from february until april) was used to produce the results in the paper.

Publication: https://bioinformatics.oxfordjournals.org/content/32/12/i201.short
doi "10.1093/bioinformatics/btw279"