Releases: TGAC/KAT
V2.4.1
v2.4.0
Overhauled dist_analysis script and automatically execute this as part of hist, gcp and comp. Statistics generated are output to stdout as well as a file called .dist_analysis.json for easy parsing in downstream tasks.
Added a new tool called 'cold' for contig length and duplication analysis. This creates a scatter plot where contigs are defined according to their length, kmer duplication rate (in assembly), kmer coverage (according to reads) and GC values.
KAT now supports gzipped fastq and fasta files natively (for k-mer counting only)
KAT can automatically trim the start of reads to a defined number of bases. This is useful for processing 10X data to avoid the barcodes on R1.
Simplified and improved build system:
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a subset of boost is kept in the KAT source tree and can be built prior to KAT with a single command: './build_boost.sh'. This version of boost will be statically linked into the KAT binaries and will NOT be installed to the system.
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Tweaked compiler options, and ensure KAT builds with GCC 5-7.
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kat python scripts are now wrapped up in a proper python package called kat. This is installed along with the kat c++ programs during install to the defined location.
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We try to statically link now to most dependencies where practical.
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Tidied up user interfaces. Removed "canonical" options, we assume the user wants canonical kmer counting by default.
v2.3.4
Fixed bug in spectra-cn plotting. Now the user has proper control over selection of cn bands.
v2.3.3
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Fixed a bug which was causing a seg fault when using the comp tool with bin sizes larger than the default value.
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Tweaked header of SECT stats output to make it clearer.
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SECT now allows includes lowercase bases in analysis.
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Added stack trace if a seg fault occurs
v2.3.2
KAT now allows users to pipe in gzipped files via process substitution.
Updated distribution analysis script to make it more robust and added calculations for estimated genome size and level of heterozygous content.
Fixed a bug in spectra hist plot title.
Fixed a bug in the help message for '-n' option in kat comp.
v2.3.1
No changes to the KAT tools themselves. This release focuses on making an improved build process. User's now have the option of disabling plotting completely, and requesting whether to link to boost in dynamic mode. We also ensure that KAT only links to python3 rather than python2 if python2 is the default python installation on the system.
v2.3.0
Added new feature to filter seq tool so that it handles paired end input. NOTE that this has required a change in the interface.
Updated documentation
Tweaked the makefiles to remove some redundancy in the compiler flags.
v2.2.0
Improved README and documentation
Better checking of python dependencies
Enforcing static linking of kat_jellyfish and kat libraries to executable
Better checking of sequence files, now kat can detect fasta and fastq files for kmer counting, even without a known extension.
v2.1.1
Updated documentation
Removed dependency on sphinx extensions in order to keep both readthedocs and homebrew happy.
Fixed representation of labels and plotting coordinates based on whether the matrix should be interpretted transposed or not.
Added shebang to python library files, in order for homebrew to be happy including them in the bin directory.
v2.1.0
KAT Release V2.1.0
Introduced new python plotting engine. Gnuplot plotting is still supported but python plotting is preferred. The plotting engine can be controlled during configuration prior to compilation.
New documentation
Testing framework change from BOOST to gtest
Travis CI support added
SECT now outputs GC counts as well as CVG counts
KAT supports SOAP scaffolder output
Various bug fixes and improvements.