KAT provides a suite of tools that, through the use of k-mer counts, help the user greet or identify issues such as determining sequencing completeness for assembly, assessing sequencing bias, identifying contaminants, validating genomic assemblies and filtering content. KAT is geared primarily to work with high-coverage genomic reads from Illumina devices, although can work with any fasta or fastq sequence place in order. Further information can be gleaned through pairwise juxtaposition of spectra, making KAT useful for WGS library comparisons and assembly validation.
We selected Jellyfish conducive to this task because it supports large K values and is one of the fastest k-mer counting programs currently available. KAT supports Unix, linux or Mac systems.
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