v2.0.8

KAT V2.0.8

Fixes for the build system.

Rename jellyfish binaries to avoid name clashes on systems that already include jellyfish.

v2.0.6

Fixes to input handling.

Updated README

v2.0.5

Enhancements to SECT, now provides richer output.

Fixed a bug when given paths to non-existent files. Previously KAT segfaulted, now if provides a proper error message.

v2.0.4

Improved handling of file groups for comp tool

Fixed an issue when checking for gnuplot in configure script.

KAT-V2.0.3

Improvements to SECT. User option to select median or mean coverage has been removed. We now output both regardedless. We also output the number of bases with non-zero count and the percentage of the sequence covered by hits.

Fixed a bug when outputting data into the current working directory for all tools.

KAT-V2.0.2

Minor fix to improve portability to Mac platforms.

KAT V2.0.1

Major overhaul of KAT. Features listed below:

• Integration of jellyfish 2, allows for K values > 31
• Jellyfish library is now embedded inside KAT, kmer counting is now done directly inside KAT meaning the user has the option (and is encouraged) to run KAT directly from FASTQ / FASTA files. This saves time and disk space to running jellyfish separately
• Auto catting of input files can be done directly on the command line... useful for when handling PE files.
• Plotting done automatically as part of all KAT tools where possible
• Plotting autoscales to likely region of interest by default
• Upgraded code to use C++11

V1.0.7

New functionality for sect: ability to request median coverage for each sequence rather than the mean. This tends to give much better results as occasionally we have a few kmers with extremely high coverage in a sequence which skews the mean coverage.

Included seqan with KAT, so that now the user doesn't need to worry about this dependency. Also has more handling for configuring the phthread library.

KAT V1.0.6

KAT V1.0.6

Changes since V1.0.5:

Changed Jellyfish dependency to V1.1.11 (currently the latest V1 release). This fixes some issues configuring KAT with jellyfish for Mac users.

Fixed a bug with the spectra-cn plots where we duplicated the entry for the highest copy number displayed before combining all together.

Added a feature to spectra-cn so that we can show cumulative increases in distinct kmers as kmer coverage increases.

KAT V1.0.5

Contains both changed for V1.0.4 which was only release internally at TGAC and V1.0.5. Details below

V1.0.5 - 28th April 2014

Removed call to auto configure when running the autogen.sh script.

Fixed issue where title could not be overriden by the user in the plotting
tools.

Changed short option name for the "list" option in spectra-mx plot tool to
'c'. This is to avoid a conflict with the "title" option.

Provided a more descriptive error message if the user enters a malformed
value for the "list" option in the spectra-mx tool.

Removed call to set the size ratio to 1 in the spectra-mx tool

V1.0.4 (internal release) - 1st April 2014

Dropped autoconf version to 2.59 to allow KAT to run in more environments.

Changed floats to doubles in sect. Previously, we may have got imprecise
mean coverage estimates when using really big sequences, such as whole
chromosome length.

Fixed spectra-cn issue, where we were not including all high copy kmers in a
final band of the spectra-cn plot.