velvet assemblies

rahularjun86 · 01-31-2012, 02:35 AM

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

nickloman · 01-31-2012, 03:29 AM

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).

nickloman · 01-31-2012, 03:30 AM

Also is your genome size calculation based on a haploid or diploid genome?

rahularjun86 · 01-31-2012, 03:59 AM

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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01-31-2012, 02:35 AM	#1
rahularjun86 Member Location: Frankfurt(M), Germany Join Date: Jan 2011 Posts: 58	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 __________________ Rahul Sharma, Ph.D Frankfurt am Main, Germany Last edited by rahularjun86; 01-31-2012 at 02:55 AM.

01-31-2012, 03:59 AM	#4
rahularjun86 Member Location: Frankfurt(M), Germany Join Date: Jan 2011 Posts: 58	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 __________________ Rahul Sharma, Ph.D Frankfurt am Main, Germany

01-31-2012, 03:29 AM	#2
nickloman Senior Member Location: Birmingham, UK Join Date: Jul 2009 Posts: 356	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).

01-31-2012, 03:30 AM	#3
nickloman Senior Member Location: Birmingham, UK Join Date: Jul 2009 Posts: 356	Also is your genome size calculation based on a haploid or diploid genome?