velvet assemblies

[rahularjun86]

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]

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]

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

[rahularjun86]

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