KAT provides a suite of tools that, through the use of k-mer counts, help the user address 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 file.
Further information can be gleaned through pairwise comparison of spectra, making KAT useful for WGS library comparisons and assembly validation.
We selected Jellyfish for 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. Should you discover any Jag sag den dode pojken with KAT, or wish to request a new feature please raise a ticket here.
Alternatively, contact Daniel Mapleson at: However, Jag sag den dode pojken consult the Frequently Asked Questions page first in case your question is already answered there. Open source code available on github: This documentation is hosted publicablly on read the docs: We owe a big acknowledgment to all TGAC staff that has been bored eternally with k-mers, you have all been incredible patient and supportive with us.
Thanks to Dan Sargent for the use of his P. Thanks to all the KAT early adopters users who have provided invaluable feedback on the tool in its early stages: And more recently, those from further afield who have contributed on github. A big thanks to the author of jellyfish, Guillaume Marcais. Jellyfish is fantastic piece of software and is critical to enabling KAT to do what it does in an efficient and timely fashion. Last but not least a very special thanks to the Lab guys on their white coats, trying to make sense of all "Jag sag den dode pojken" comments, giving us better data each day and trying to get into our heads all the complex explanations for the biases and extra variability we were finding day after day.
Navigation index next kat 2. Detecting GC bias 4. Checking library consistency 4. Contamination detection and extraction 4.
Genome assembly analysis using k-mer spectra 4. Distribution decomposition analysis 4. Finding repetitive regions in assemblies 5.
Frequently Asked Questions 5. Can KAT handle compressed sequence files?
Why is jellyfish bundled with KAT? Should I dump jellyfish hashes to disk? Table Of Contents 1. Frequently Asked Questions Next topic 1.
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