Hello,
We plan on resequencing a hybrid genotype of poplar (genome size~ 430Mb) and sequencing de novo a hybrid genotype of eucalyptus (genome size~ 580Mb). We would like to do as many lines as possible per lane. We plan on using the Illumina HiSeq3000 platform which outputs about 300 million paired end reads per output. Is 30X good enough for de novo? and 15X good enough for resequencing? There is a published genome for our hybrid poplar genotype.
Hi Estefania,
You should try to get a higher coverage for both experiments. A de novo assembly of a plant genome sequence would be much better with about 80X coverage. Additionally, it would be useful to generate some large insert mate pair data to increase the continuity of your assembly.
Resequencing could benefit from an increased coverage as well. This would improve the quality of called variants. 30-40x might be a good range if you use a single sample.
Good luck with your assembly!
How did your assembly go? I'm curious since I haven't done any sequencing on plant genomes. For vertebrate genomes, 15X-30X is generally good enough. I recently saw a tweet that a group in Australia was also doing some eucalyptus sequencing.
Jason Travis Howard
For a single Pseudomonas aeruginosa bacterium, I got 24x coverage by using Illumina MiSeq. Is it good?
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