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Total Length Of Assembled Scaffolds Is Greater Than Genome Length

Hi,

I would greatly appreciate some help with my problem.

I have just assembled denovo a genome from Illumina 100bp paired end reads, using SOAPdenovo2 and then GapCloser.

My total scaffold length is 1,062,995,336 base pairs (from 207528 scaffolds) and my haploid genome is approximately 1.2 Gb. From this I calculate a percentage coverage of 104%?

Have I calculated coverage incorrectly, or should I have filtered short scaffolds? I am unsure why the coverage is greater than 100%?

Thanks very much for any help

Alison

coverage denovo genome assembly
• 4,426 views • link
updated by ugly.betty77 ugly.betty77 • written by AW AW

How did you calculate 104%? from what you've said, your assembly is 1.06 Gb in size, and you are expecting 1.2 Gb so wouldn't your coverage be 88% (1.06/1.2)?

• 95 views • link
written by cts cts

2 answers

What I would do would be to align the raw reads back to your scaffolds then genotype to compute your coverage.

• 0 views • link
written by Gabriel R. Gabriel R.

For one assembly I have been doing currently, I experienced similar problem with SGA. Jared Simpson recommended me to remove anything smaller than 2x read length to avoid polymorphic or repetitive being over-counted. After I removed those short scaffolds, the total size of assembly came to be close to what I got from other assemblers.

• 0 views • link
written by ugly.betty77 ugly.betty77

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