From contigs towards chromosomes: automatic Improvement of Long Read Assemblies (ILRA)

Ruiz, José Luis; Reimering, Susanne; Sanders, Mandy; Escobar-Prieto, Juan David; Brancucci, Nicolas M. B.; Echeverry, Diego F.; Abdi, Abdirahman; Marti, Matthias; Gómez‐Díaz, Elena; Otto, Thomas D.

doi:10.5281/zenodo.7516750

2023

DOI: 10.5281/zenodo.7516750

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From contigs towards chromosomes: automatic Improvement of Long Read Assemblies (ILRA)

José Luis Ruiz

Susanne Reimering

Mandy Sanders

et al.

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From contigs towards chromosomes: automatic Improvement of Long Read Assemblies (ILRA)

Ruiz

Reimering

Sanders

et al. 2021

Preprint

Self Cite

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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.

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From contigs towards chromosomes: automatic Improvement of Long Read Assemblies (ILRA)

Ruiz

Reimering

Sanders

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

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From contigs towards chromosomes: automatic Improvement of Long Read Assemblies (ILRA)

Cited by 1 publication

References 0 publications

From contigs towards chromosomes: automatic Improvement of Long Read Assemblies (ILRA)

From contigs towards chromosomes: automatic Improvement of Long Read Assemblies (ILRA)

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