I have the simplest task for a de novo assembler: to assemble a short bacterial 10kb plasmid without repeats from Illumina 90 bp long reads. The plasmid was sequenced on average 1,000 times over. I used default parameters on velvet and SeqMan NGen and couldn't get it assembled. Could anyone suggest an assembler and parameters that I could use for the task.
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Originally posted by pmiguel View PostFirst throw away 90% of your reads. 1000x is too high.
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Phillip
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Originally posted by e.dobbs View PostI have a similar project to this one and I'm having trouble assembling my viral sequences which I'm expecting 10,000-100,000x coverage. Why does too much coverage produce a problem for de novo assembly?
Travis
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Originally posted by e.dobbs View PostI have a similar project to this one and I'm having trouble assembling my viral sequences which I'm expecting 10,000-100,000x coverage. Why does too much coverage produce a problem for de novo assembly?
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Phillip
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