Question: Denovo sequencing of species in different locations
1
gravatar for biocon
5 months ago by
biocon10
biocon10 wrote:

Dear Biostars,

I have sequenced a genome of a animal in two different locations. The first one has 8 different lanes and the second has 10. I needed to perform the denovo assembly of this animal species and I was trying to perform assembly of each lane (which will be 8+10=18 aseembly) with the help of SOAPdenovo and GAM-NGS used for merging the contigs. Is this the right way or is there any other method/suggestion for this ?

denovo next-gen assembly • 142 views
ADD COMMENTlink modified 5 months ago by WouterDeCoster44k • written 5 months ago by biocon10
2

Having overly high coverage of data can be detrimental to assemblies as well (what is the genome size you are working with). If you feel that is the case then you could try normalizing your data first.

ADD REPLYlink modified 5 months ago • written 5 months ago by genomax85k
1
gravatar for WouterDeCoster
5 months ago by
Belgium
WouterDeCoster44k wrote:

It would probably be better to have all reads available for your assembler at the same time, so I would not split per lane and just combine all data.

ADD COMMENTlink written 5 months ago by WouterDeCoster44k

Due to size I spitted the data. If I combine all the lanes, the read size will more than 100 GB of size

ADD REPLYlink modified 5 months ago • written 5 months ago by biocon10

Of course, you will need to have enough RAM for your assembly. I also don't know the genome size of your organism and as such the theoretical coverage you obtained.

ADD REPLYlink written 5 months ago by WouterDeCoster44k
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