ArticleBriefings in bioinformatics2023
From contigs towards chromosomes: automatic improvement of long read assemblies (ILRA).
Article in Briefings in bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 13 citations in OpenAlex.
- upsML: A high-accuracy machine learning classifier for predicting Plasmodium falciparum var gene upstream groups.PloS one · 2026Article
- Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut.Nature communications · 2025Article
- Comparison of nanopore with illumina whole genome assemblies of the Epstein-Barr virus in Burkitt lymphoma.Scientific reports · 2025Article
- Comparison of Nanopore with Illumina Whole Genome Assemblies of the Epstein-Barr Virus in Burkitt Lymphoma.medRxiv : the preprint server for health sciences · 2025Article
- Supersaturation mutagenesis reveals adaptive rewiring of essential genes among malaria parasites.Science (New York, N.Y.) · 2025Article
- Genome drafts ofMicrobiology resource announcements · 2025Article
- Long-Read Sequencing andBiology · 2024Article
- Highly accurate genome assembly of an improved high-yielding silkworm strain, Nichi01.G3 (Bethesda, Md.) · 2023Article
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Authors and funding
9 authors at 6 institutions in 6 countries.
Funding
Abstract
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.