Kermit: linkage map guided long read assembly

Abstract

Background With long reads getting even longer and cheaper, large scale sequencing projects can be accomplished without short reads at an affordable cost. Due to the high error rates and less mature tools, de novo assembly of long reads is still challenging and often results in a large collection of contigs. Dense linkage maps are collections of markers whose location on the genome is approximately known. Therefore they provide long range information that has the potential to greatly aid in de novo assembly. Previously linkage maps have been used to detect misassemblies and to manually order contigs. However, no fully automated tools exist to incorporate linkage maps in assembly but instead large amounts of manual labour is needed to order the contigs into chromosomes.Results We formulate the genome assembly problem in the presence of linkage maps and present the first method for guided genome assembly using linkage maps. Our method is based on an additional cleaning step added to the assembly. We show that it can simplify the underlying assembly graph, resulting in more contiguous assemblies and reducing the amount of misassemblies when compared to de novo assembly.Conclusions We present the first method to integrate linkage maps directly into genome assembly. With a modest increase in runtime, our method improves contiguity and correctness of genome assembly.

Chromonomer: A Tool Set for Repairing and Enhancing Assembled Genomes Through Integration of Genetic Maps and Conserved Synteny

“…Lep-Anchor (Rastas 2020) also aims to optimize marker order, first employing a Hidden Markov Model to bin markers to different linkage groups and split inter-linkage group scaffolds, and then it uses dynamic programming to calculate the number of markers that support all particular scaffold orders. The Kermit software uses a genetic map to guide a de novo assembly (Walve et al 2019). Kermit bins scaffolds given in an initial assembly according to their order in the genetic map, then it places raw, long reads into those bins and creates an overlap graph from that initial order.…”

HGGA: hierarchical guided genome assembler

“…KOOTA [ 10 ] maps reads to an optical map and uses the mapping positions to produce a positional de Bruijn graph which is less tangled than a regular de Bruijn graph. Kermit [ 11 ] maps reads to a genetic linkage map and then uses this information to remove edges that conflict with a genetic linkage map from the assembly graph of miniasm [ 1 ]. OpticalKermit [ 12 ] is a modification of Kermit to use optical maps instead of genetic linkage maps.…”

“…In our previous work, we introduced Kermit [ 11 ], a method for guiding an assembly with a genetic linkage map instead of a reference sequence. Genetic linkage maps are a technique to orient and place contigs within a chromosome and to detect misassembled contigs.…”

Genomic Resource Development for Hydrangea (Hydrangea macrophylla (Thunb.) Ser.)—A Transcriptome Assembly and a High-Density Genetic Linkage Map

“…To date, only one linkage map was reported in hydrangea, but with low SSR marker density [13], which is much lower than the number of linkage maps reported in roses (eight) [14], peony (three) [15], and chrysanthemum (three) [16]. In addition to providing tools for MAS, high-density linkage maps could also be used to assist genome assembly in scaffolding and quality assessments [17]. Further marker development and high-density genetic linkage maps are needed for potential genetic improvement as well as genomic studies in hydrangea.…”