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 ?
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written
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biocon •
1 answer
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.
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.
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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.