We developed SASAR (“Super-ASsembly” from Assembly Reconciliation) as a meta-assembly tool to reconcile the result of different assemblies obtained from Nanopore long read sequencing data.

Given the intraspecific variability of plant genomes notably due to transposable element activity and copy number variation, reference genomes cannot capture the extent of individual genomic variation. Therefore high quality genome assemblies are needed in plant biology. Different computational tools have recently been developed to perform genome assemblies using long reads. However, each tool has its specific performance in terms of number of contigs and total assembly length. Here we developed SASAR (“Super-ASsembly” from Assembly Reconciliation) as a meta-assembly tool to reconcile the result of different assemblers. Using Oxford Nanopore Technology (ONT) sequencing of Arabidopsis thaliana Columbia , we provide a chromosome-arm level assembly with a total length approximately 10 Mb longer than TAIR10.1, filling 73% N-stretches of the reference genome TAIR10.1. For the rice O. sativa Nipponbare, our assembly closed 16% of non-centromeric N-stretches of the reference genome IRGSP-1. We further demonstrate that the SASAR tool enables the reliable detection of new transposable elements insertions in a rice T-DNA insertion line. This tool will help researchers interested in using the ONT technology to quickly assemble the genome of their plant line or accession of interest.