v2 2021 compilation

not a new release, just a change in the compilation system

v2.3.3

forgot the -O3 flag in the previous version, hence DSK was slower than it should have been. Fixed.

v2.3.1

No new features, just a collection of bugfixes accumulated since last year

v2.3.0

Many new features and bug fixes since latest official release, including:

• Switching gatb-core version from 1.2.1 to 1.4.1 (see the details in file thirdparty/gatb-core/gatb-core/RELEASES.md or on the github releases page). Importantly for DSK :

  • Faster k-mer counting (inspired by KMC3 but not yet as fast :).
  • Compiling GATB-Core library now requires c++/11 capable compilers.
  • CMake 3.1.0 is the minimum release of CMake required to compile GATB-Core.
  • Bug fixes in some multi-threaded situations.

• Some new features (also coming from updates in gatb-core but not yet in an official gatb-core release):

  • An easier way to plot the kmer abundance profile (option -histo and R script in the utils/ directory).
  • New feature: can output kmer count abundance matrix between a genome assembly and sequencing read datasets to plot a kmer comparison plot, inspired by KAT (Kmer Analysis Toolkit) (option -histo2D and R script in the utils/ directory).
  • New custom solidity option to output kmers specific to a subset of the input files. (-solidity-custom).

v2.2.0

This is a bugfix release since 2.1.0. No new features. More stability.

Note: in the binary release tar file, the correct simple_test.sh script is in the test/ folder.

Thanks to Hamid Mohamadi for noting a mistake in the README.

v1.0.6

initial github release. disregard the version name, this is DSK v2 not v1.