Hi,
I'm trying to de novo assembly the genome of a non-model mammalian species with a relatively large genome (~3 Gb) for which we have a relatively close reference - average 5% divergent (~12 My). What I was wondering is if there is any way I can take advantage of this relatively close reference to assemble my genome and in that case what would be the best strategy.
One of things I thougth was to first do the de novo assembly of my genome (in allpaths-lg, for which the data was specially tailored) and then to use the reference to help scaffolding the contigs/scaffolds resulting from the de novo assembly - i'm aware that, for instance, AlignGraph is designed for this task. Could this be a good solution or is there any other tool available (not that I don't want to use AlignGraph but I want to be aware of the possible tools)?
Thanks,
Fernando
I'm trying to de novo assembly the genome of a non-model mammalian species with a relatively large genome (~3 Gb) for which we have a relatively close reference - average 5% divergent (~12 My). What I was wondering is if there is any way I can take advantage of this relatively close reference to assemble my genome and in that case what would be the best strategy.
One of things I thougth was to first do the de novo assembly of my genome (in allpaths-lg, for which the data was specially tailored) and then to use the reference to help scaffolding the contigs/scaffolds resulting from the de novo assembly - i'm aware that, for instance, AlignGraph is designed for this task. Could this be a good solution or is there any other tool available (not that I don't want to use AlignGraph but I want to be aware of the possible tools)?
Thanks,
Fernando
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