instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder
Baudry, L.; Guiglielmoni, N.; Marie-Nelly, H.; Cormier, A.; Marbouty, M.; Avia, K.; Mie, Y.L.; Godfroy, O.; Sterck, L.; Cock, J.M.; Zimmer, C.; Coelho, S.M.; Koszul, R. (2020). instaGRAAL: chromosome-level quality scaffolding of genomes using a proximity ligation-based scaffolder. Genome Biol. 21(1): 148. https://hdl.handle.net/10.1186/s13059-020-02041-z
In: Genome Biology. BMC: London. ISSN 1465-6906; e-ISSN 1474-760X, more
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| Keywords |
Desmarestia herbacea (Turner) J.V.Lamouroux, 1813 [WoRMS]; Ectocarpus Lyngbye, 1819 [WoRMS]
Marine/Coastal |
| Author keywords |
Ectocarpus; Hi-C scaffolding; Hi-C; genome assembly; MCMC; GPU; Desmarestia herbacea |
| Authors | | Top |
- Baudry, L.
- Guiglielmoni, N., more
- Marie-Nelly, H.
- Cormier, A.
- Marbouty, M.
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- Avia, K.
- Mie, Y.L.
- Godfroy, O.
- Sterck, L., more
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- Cock, J.M.
- Zimmer, C.
- Coelho, S.M.
- Koszul, R.
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| Abstract |
Hi-C exploits contact frequencies between pairs of loci to bridge and order contigs during genome assembly, resulting in chromosome-level assemblies. Because few robust programs are available for this type of data, we developed instaGRAAL, a complete overhaul of the GRAAL program, which has adapted the latter to allow efficient assembly of large genomes. instaGRAAL features a number of improvements over GRAAL, including a modular correction approach that optionally integrates independent data. We validate the program using data for two brown algae, and human, to generate near-complete assemblies with minimal human intervention. |
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