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
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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