Benchmarking of Hi-C tools for scaffolding de novo genome assemblies
Obinu, L.; Trivedi, U.; Porceddu, A.
Show abstract
The implementation of Hi-C reads in the de novo genome assembly allows to order large regions of the genome in scaffolds, obtaining chromosome-level assemblies. Several bioinformatics tools have been developed for genome scaffolding with Hi-C, and all have pros and cons which need to be carefully evaluated before adoption. We developed assemblyQC, a bash pipeline that combines QUAST, BUSCO, Merqury and, optionally, Liftoff, plus a gene positioning validation script to evaluate and benchmark the performance of three scaffolders, 3d-dna, SALSA2, and YaHS, on two de novo assembly of Arabidopsis thaliana obtained from the same raw PacBio HiFi and ONT data. In our analysis, YaHS proved to be the best-performing bioinformatic tool for scaffolding of de novo genome assembly.
Matching journals
The top 5 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- An improved chromosome-level genome assembly of perennial ryegrass (Lolium perenne L.) 97%
- Chromosome-scale assembly of the highly heterozygous genome of red clover (Trifolium pratense L.), an allogamous forage crop species 96%
- Optimizing experimental design for genome sequencing and assembly with Oxford Nanopore Technologies 95%
Similar papers in this journal
- High-fidelity (repeat) consensus sequences from short reads using combined read clustering and assembly 96%
- Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection. 95%
- GenomeQC: A quality assessment tool for genome assemblies and gene structure annotations 95%
Similar papers in this journal
"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.