Hi guys,
i have a question regarding denovo assembly.
Firstly some info on my machine:
64 bit Slackware linux
64GB RAM
i7 3930 K
For a small genomes there is no problem. But what about 3Gb genomes? How can one handle such a task considering the available power of the working machine?
Once i had a RNAseq with 70M PE illumina reads which i tried to assemble with SOAPdenovo-trans but the program broke after loading 100M reads.So i am concerned that for a 3Gb genome with 10x coverage at least i will have a huge number of reads which i wont be able to handle with SOAP-denovo. I saw that they have a '-a' option for the pregraph which supposedly would restrict the memory usage but i have the feeling i will have problems.
Then i was having the idea to split the raw reads into smaller files and make mini denovo assemblies on the split reads and then merge them somehow. But for now i could not find software which could allow me to do that.
So i would like to ask if there is such software which will allow me to do the procedure described above? Or is there some other strategy to tackle that problem? Or i just need a machine with loots of RAM?
Thank you for your time and any help!!
i have a question regarding denovo assembly.
Firstly some info on my machine:
64 bit Slackware linux
64GB RAM
i7 3930 K
For a small genomes there is no problem. But what about 3Gb genomes? How can one handle such a task considering the available power of the working machine?
Once i had a RNAseq with 70M PE illumina reads which i tried to assemble with SOAPdenovo-trans but the program broke after loading 100M reads.So i am concerned that for a 3Gb genome with 10x coverage at least i will have a huge number of reads which i wont be able to handle with SOAP-denovo. I saw that they have a '-a' option for the pregraph which supposedly would restrict the memory usage but i have the feeling i will have problems.
Then i was having the idea to split the raw reads into smaller files and make mini denovo assemblies on the split reads and then merge them somehow. But for now i could not find software which could allow me to do that.
So i would like to ask if there is such software which will allow me to do the procedure described above? Or is there some other strategy to tackle that problem? Or i just need a machine with loots of RAM?
Thank you for your time and any help!!
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