Hi,
I'm new to genome assembly, and am having problems.
I will be grateful for tips on how to assemble a bacterial genome.
I have 100bp hiseq illumina data. Genome size is ~4MB.
I have been using Dynamic Trim, then LengthSort, then velvet or soapdenovo.
The problem is that after running velvet, I get an N50 of 1Mb , but the total size of the genome come to 30MB, over 6 times more than it should.
A friend suggested using a subsection of the data I have (cause I have 350x coverage for one of my genomes and 3048x coverage for another). I've even tried that but the total size of the genome is still more than it should be.
Any help would be greatly appreciated!!
I'm new to genome assembly, and am having problems.
I will be grateful for tips on how to assemble a bacterial genome.
I have 100bp hiseq illumina data. Genome size is ~4MB.
I have been using Dynamic Trim, then LengthSort, then velvet or soapdenovo.
The problem is that after running velvet, I get an N50 of 1Mb , but the total size of the genome come to 30MB, over 6 times more than it should.
A friend suggested using a subsection of the data I have (cause I have 350x coverage for one of my genomes and 3048x coverage for another). I've even tried that but the total size of the genome is still more than it should be.
Any help would be greatly appreciated!!
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