Plasmodium falciparum Genome sequencing and assembly from PacBio. Plasmodium falciparum

Recent advances in long read technologies not only enable large consortia to aim to sequence all eukaryotes on Earth, but they also allow individual laboratories to sequence their species of interest with relatively low investment. Although there is a promise to obtain 'perfect genomes' with long read technologies, the number of contigs often exceeds the number of chromosomes by far, containing many insertion and deletion errors around homopolymer tracks. To overcome these issues, we implemented the ILRA pipeline to correct long read-based assemblies, so contigs are reordered, renamed, merged, circularized, or filtered if erroneous or contaminated, and Illumina reads are used to correct homopolymer errors. We successfully tested our approach to improve the genomes of four novel Plasmodium falciparum assemblies from field samples. PacBio RSII assemblies in PRJNA714074. PacBio Sequel assemblies in PRJNA757237.