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Old 01-31-2012, 01:35 AM   #1
rahularjun86
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Unhappy velvet assemblies

Dear all,
I am doing an assembly of 40 Mb genome with expected coverage of 181x. I am using Illumina reads 76bp length with insert size 200 bp (Sd 20 bp). I have tried velvet for these assemblies and 86-99% of reads were used in this assembly with N50 of 80kb (with k-mer's 21,55,2). But the strange thing is that I am getting only 19 Mb genome after all assemblies. According to the staff whole genome has been covered during the library preparations.

And secondly, should I turn off the velvet scaffolding before minimus2 assemblies/scaffolding??

I would appreciate your suggestions.

Thanks in advance
Rahul
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Last edited by rahularjun86; 01-31-2012 at 01:55 AM.
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Old 01-31-2012, 02:29 AM   #2
nickloman
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Assuming the genome is truly 40Mb, the most likely explanation is the presence of repeats.

Try doing a plot of contig length versus k-mer coverage which will help you visualise the repeat structure of your genome (use the values in stats.txt produced by Velvet).
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Old 01-31-2012, 02:30 AM   #3
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Also is your genome size calculation based on a haploid or diploid genome?
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Old 01-31-2012, 02:59 AM   #4
rahularjun86
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Dear Nickloman, thank you so much for your reply. I am plotting the contig length vs k-mer coverage. It is haploid genome.
Thanks,
Rahul
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