TandemMapper and TandemQUAST: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats

Abstract

Extra-long tandem repeats (ETRs) are widespread in eukaryotic genomes and play an important role in fundamental cellular processes, such as chromosome segregation. Although emerging long-read technologies have enabled ETR assemblies, the accuracy of such assemblies is difficult to evaluate since there is no standard tool for their quality assessment. Moreover, since the mapping of long error-prone reads to ETR remains an open problem, it is not clear how to polish draft ETR assemblies. To address these problems, we developed the tandemMapper tool for mapping reads to ETRs and the tandemQUAST tool for polishing ETR assemblies and their quality assessment. We demonstrate that tandemQUAST not only reveals errors in and evaluates ETR assemblies, but also improves them. To illustrate how tandemMapper and tandemQUAST work, we apply them to recently generated assemblies of human centromeres.

Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies

“…However, many of QUAST's metrics are based on the reference alignment, which incorrectly reports true variants in the assembled genome as potential mis-assemblies. A recent extension to the QUAST toolkit combines evidence from both k-mers and long reads to better identify certain classes of structural mis-assembly [19].…”

A survey of k-mer methods and applications in bioinformatics

“…This process commonly utilizes k-mers to build De Bruijn graphs or implements overlap-layout-consensus methods. Allpaths-LG [239] , Bifrost [240] , Canu [241] , Cortex [242] , ELBA [243] , KAT [223] , MEGAHIT [244] , Merqury [46] , QUAST-LG [245] , SKESA [246] , SPAdes [75] , TandemQUAST [247] , TandemMapper [248] Sequence Comparison Alignment-free methods are increasingly used for DNA and protein sequence comparison since they are much faster than traditional alignment-based approaches. Most alignment-free algorithms are based on the word or k-mer composition of the sequences under study.…”

Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time

“… Landmarks in human satellite DNA research. The depicted timeline represents the knowledge evolution of satellite DNA biology in terms of classification, representativity, and significance, as well as the potential future and ongoing character of substantial breakthroughs in the area [ 7 , 9 , 10 , 29 , 30 , 31 , 45 , 46 , 51 , 52 , 53 , 58 , 73 , 74 , 75 , 79 , 87 , 92 , 96 , 107 , 117 , 120 , 127 , 128 , 150 , 162 , 173 , 184 , 185 , 186 , 187 , 188 , 190 , 191 , 192 , 193 , 194 , 195 , 196 , 197 , 198 , 199 ]. …”