Nanopore-based de novo genome assembly of Biscogniauxia marginata
Genomic DNA from a 2-week old culture was extracted using a previously described CTAB-based protocol (https://doi.org/10.1007/s11046-019-00404-0), subsequently quality and quantity of gDNA was assessed by TapeStation (Genomic DNA Screen Tape) and 1000ng was subjected to library preparation with the Oxford Nanopore Technologies native ligation kit SQK-LSK114. The final library was loaded onto a MinION Flowcell R10.4.1 (GridION). Data with a Q-value of 10 or higher were collected after dorado basecalling in the super accuracy mode. All FASTQ data was collected into a single file and processed via chopper (fragments equal or larger of 1100bp and a Q of 10 and higher; thereafter 50bp of head and tail of each sequence were removed). Flye v.2.9.5 was used to generate the de novo genome assembly.