Parameter exploration improves the accuracy of long-read genome assembly
Priyam, A.; Witwicka, A.; Brahma, A.; Stolle, E.; Wurm, Y.
Show abstract
Long-molecule sequencing is now routinely applied to generate high-quality reference genome assemblies. However, datasets differ in repeat composition, heterozygosity, read lengths and error profiles. The assembly parameters that provide the best results could thus differ across datasets. By integrating four complementary and biologically meaningful metrics, we show that simple fine-tuning of assembly parameters can substantially improve the quality of long-read genome assemblies. In particular, modifying estimates of sequencing error rates improves some metrics more than two-fold. We provide a flexible software, CompareGenomeQualities, that automates comparisons of assembly qualities for researchers wanting a straightforward mechanism for choosing among multiple assemblies.
Matching journals
The top 5 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Near-chromosomal de novo assembly of Bengal tiger genome reveals genetic hallmarks of apex-predation 94%
- Accurate assembly of the olive baboon (Papio anubis) genome using long-read and Hi-C data 94%
- The draft nuclear genome assembly of Eucalyptus pauciflora: new approaches to comparing de novo assemblies 94%
Similar papers in this journal
- Long-read sequencing and genome assembly of natural history collection samples and challenging specimens 96%
- Automated assembly scaffolding elevates a new tomato system for high-throughput genome editing 96%
- Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL, a proximity ligation-based scaffolder 95%
Similar papers in this journal
Similar papers in this journal
- Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long read data 96%
- Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection 95%
- A chromosome-level assembly of the cat flea genome uncovers rampant gene duplication and genome size plasticity 94%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.