Meloidogyne incognita genome assembly

We first used guppy-v6.0.6 in super high-accuracy mode with a minimal quality score of 7 (--min_qscore 7) to base-call reads from the raw sequencing signal. Following QC, we used nanofilt (De Coster et al., 2018) to crop the 50 first and the 30 last nucleotides as these regions showed reduced per-base quality. We then selected reads that were at least 2kb long and had a quality score Q > 12. This returned 1,709,063 cleaned reads for M. incognita. We assembled the genomes from ONT cleaned data using NECAT (Chen et al., 2021) with default parameters and an input genome size of 200Mb. After M. incognita assembly and bridging, NECAT formed 298 contigs for a genome size of 199,975,050 bp and a N50 length of 1,856,931 (longest contig = 4,672,579 bp, L50#= 37). We further removed the contigs corresponding to the mitochondrial genome of M. incognita. The final number of contigs is 291.