Recent advances in long read technologies not only enable 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 number of contigs often exceeds the number of chromosomes significantly, containing many insertion and deletion errors around homopolymer tracks. To overcome these issues, we implemented ILRA to correct long reads-based assemblies, a pipeline that orders, names, merges, and circularizes contigs, filters erroneous small contigs and contamination, and corrects homopolymer errors with Illumina reads. We successfully tested our approach to assemble the genomes of four novel Plasmodium falciparum samples, and on existing assemblies of Trypanosoma brucei and Leptosphaeria spp. We found that correcting homopolymer tracks reduced the number of genes incorrectly annotated as pseudogenes, but an iterative correction seems to be needed to reduce high numbers of homopolymer errors. In summary, we described and compared the performance of a new tool, which improves the quality of long read assemblies. It can be used to correct genomes of a size of up to 300 Mb.

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. Long read technologies embody the promise of overcoming scaffolding problems associated with repeats and low complexity sequences, but the number of contigs often far exceeds the number of chromosomes and they may contain many insertion and deletion errors around homopolymer tracts. To overcome these issues, we have implemented the ILRA pipeline to correct long read-based assemblies. Contigs are first reordered, renamed, merged, circularized, or filtered if erroneous or contaminated. Illumina short reads are used subsequently to correct homopolymer errors. We successfully tested our approach by improving the genome sequences of Homo sapiens, Trypanosoma brucei, and Leptosphaeria spp., and by generating four novel Plasmodium falciparum assemblies from field samples. We found that correcting homopolymer tracts reduced the number of genes incorrectly annotated as pseudogenes, but an iterative approach seems to be required to correct more sequencing errors. In summary, we describe and benchmark the performance of our new tool, which improved the quality of novel long read assemblies up to 1 Gbp. The pipeline is available at GitHub: https://github.com/ThomasDOtto/ILRA.

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