De novo genome assemblies for Plasmodium falciparum

Advances in long read technologies have not only enabled large consortia to aim to sequence all eukaryotes on Earth, but they also allow many laboratories to sequence their species of interest. Although there is a promise to obtain “perfect genomes” with long read technologies, the outcome of many assemblies is still around 100 contigs, including containing many insertions and deletions errors around homopolymer tracks. Thus, it still requires several steps to obtain high-quality assemblies. We generated a pipeline to automatically improve long reads genome assemblies.We described and compared the performance of a new tool, the IPA pipeline, which generally improves the quality of the sequences. We used it to improve several genomes assemblies, including four novel P. falciparum genomes.