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20 avril 2023
- doi: 10.57745/50YQVI
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Agricultural SciencesSujets proches
Meloidogyne javanica Mitochondrial genomes mtDNA Mitochondrial genome Natural science Sciences Science of science Phosphonucleosides Pottery pillows Porcelain pillows ChenCiter ce document
Ana Paula Zotta Mota et al., « Meloidogyne javanica genome assembly », Recherche Data Gouv, ID : 10.57745/50YQVI
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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 11,506,089 cleaned reads for M. javanica. We assembled the genomes from ONT cleaned data using NECAT (Chen et al., 2021) with default parameters and an input genome size of 300Mb. We obtained 365 contigs with an assembly size of 298,215,187 bp and a N50 of 2,079,353. After the removal of the mitochondrial genome, we had a final assembly with 364 contigs