KAT: A K-mer Analysis Toolkit to quality control NGS datasets and genome assemblies

Abstract

Motivation: De novo assembly of whole genome shotgun (WGS) next-generation sequencing (NGS) data benefits from high-quality input with high coverage. However, in practice, determining the quality and quantity of useful reads quickly and in a reference-free manner is not trivial. Gaining a better understanding of the WGS data, and how that data is utilized by assemblers, provides useful insights that can inform the assembly process and result in better assemblies. Results: We present the K-mer Analysis Toolkit (KAT): a multi-purpose software toolkit for reference-free quality control (QC) of WGS reads and de novo genome assemblies, primarily via their k-mer frequencies and GC composition. KAT enables users to assess levels of errors, bias and contamination at various stages of the assembly process. In this paper we highlight KAT's ability to provide valuable insights into assembly composition and quality of genome assemblies through pairwise comparison of k-mers present in both input reads and the assemblies.

An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps

“…The remaining 152 contigs which were not scaffolded in the 12 chromosomes were stitched together to create chromosome 00 (9.6 Mbp) with a 100 bp gap inserted between adjacent contigs. Genome assemblies can be validated for completeness by comparing the k-mer's present in the raw genomic DNA-Seq reads with those in the genome assembly (Mapleson et al 2017). The kmer spectra of SL4.0 genome assembly shows a single homozygous peak at the expected (20x) coverage based on k-mer analysis (Suppl.…”

Improved genome assembly and annotation of the soybean aphid (Aphis glycinesMatsumura)

“…These data were derived from a lab reared colony of biotype 4 which was unlikely to be contaminated by parasitoid wasp larvae. The Canu assembly was checked for contamination by creating a GC-content coverage plot using KAT sect from the K-mer analysis toolkit (KAT) (Mapleson et al 2017). For this analysis, all biotype 4 Illumina MiSeq libraries from Wenger et.…”

An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations

“…A KAT k-mer spectra copy number plot provides information to analyze how much and what type of k-mer content from reads is present in an assembly (Mapleson et al 2017). It decomposes the kmer spectrum of a read data set by the frequency in which the kmers are encountered in the assembly.…”

“…Contigs were scaffolded using the PE, LMP, and TALL reads and the SOAPdenovo2 (Luo et al 2012) prepare→map→scaffold pipeline, run at k = 71. Contigs and scaffolds were quality controlled using KAT spectra-cn plots (Mapleson et al 2017) to assess motif representation.…”