Chromosome-level quality scaffolding of brown algal genomes using InstaGRAAL, a proximity ligation-based scaffolder
Résumé
Hi-C has become a popular technique in recent genome assembly projects. Hi-C exploits
contact frequencies between pairs of loci to bridge and order contigs in draft genomes,
resulting in chromosome-level assemblies. However, application of this approach is currently
hampered by a lack of robust programs that are capable of effectively treating this type of
data, particularly open source programs. We developed instaGRAAL, a complete overhaul
of the GRAAL program, which has adapted the latter to allow efficient assembly of large
genomes. Both GRAAL, and instaGRAAL use a Markov Chain Monte Carlo algorithm to
perform Hi-C scaffolding, but instaGRAAL features a number of improvements including a
modular polishing approach that optionally integrates independent data. To validate the
program, we used it to generate chromosome-level assemblies for two brown algae,
Desmarestia herbacea and the model Ectocarpus sp., and quantified improvements
compared to the initial draft for the latter. Overall, instaGRAAL is a program able to generate,
using default parameters with minimal human intervention, near-complete assemblies.
| Origine | Fichiers produits par l'(les) auteur(s) |
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