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Link to papers for minimum coverage needed, add motivation to not use…
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… Illumina for correction. Issue #1187.
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brianwalenz committed Dec 21, 2018
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Expand Up @@ -327,8 +327,17 @@ Why do I get less corrected read data than I asked for?
What is the minimum coverage required to run Canu?
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For eukaryotic genomes, coverage more than 20X is enough to outperform current hybrid
methods. Below that, you will likely not assemble the full genome.
methods. Below that, you will likely not assemble the full genome. The following
two papers have several examples.
* `Koren et al. (2013) Reducing assembly complexity of microbial genomes with single-molecule sequencing <https://www.ncbi.nlm.nih.gov/pubmed/24034426>`_
* `Koren and Walenz et al. (2017) Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation <https://www.ncbi.nlm.nih.gov/pubmed/28298431>`_

Can I use Illumina data too?
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No. We've seen that using short reads for correction will homogenize repeats and
mix up haplotypes. Even though the short reads are very high quality, their length
isn't sufficient for the true alignment to be identified, and so reads from other repeat
instances are used for correction, resulting in incorrect corrections.

My circular element is duplicated/has overlap?
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