| Summary: | Antimalarial drug resistance has become a real public health problem despite WHO measures. New sequencing technologies make it possible to investigate genomic variations associated with resistant phenotypes at the genome-wide scale. Based on the use of hemisynthetic nanopores, the PromethION technology from Oxford Nanopore Technologies can produce long-read sequences, in contrast to previous short-read technologies used as the gold standard to sequence Plasmodium. Two clones of <i>P. falciparum</i> (<i>Pf</i>3D7 and <i>Pf</i>W2) were sequenced in long-read using the PromethION sequencer from Oxford Nanopore Technologies without genomic amplification. This made it possible to create a processing analysis pipeline for human <i>Plasmodium</i> with ONT Fastq only. <i>De novo</i> assembly revealed N50 lengths of 18,488 kb and 17,502 kb for the <i>Pf</i>3D7 and <i>Pf</i>W2, respectively. The genome size was estimated at 23,235,407 base pairs for the <i>Pf3D7</i> clone and 21,712,038 base pairs for the <i>Pf</i>W2 clone. The average genome coverage depth was estimated at 787X and 653X for the <i>Pf</i>3D7 and <i>Pf</i>W2 clones, respectively. This study proposes an assembly processing pipeline for the human <i>Plasmodium</i> genome using software adapted to large ONT data and the high AT percentage of <i>Plasmodium</i>. This search provides all the parameters which were optimized for use with the software selected in the pipeline.
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