Hi,
I am mostly comfortable with DNA resequencing, mRNAseq, ChIPseq, etc. data. And always feel difficult handling de novo assembly works. But it comes my way anyway.
I have a set of data that are mate pair sequencing of a ~1GB genome. It is close to 30x coverage after linker being removed. the insert size is about 8Kb. I don't feel it is a good idea to use mate pair only (I'd rather to have various sized libraries). Without evidence, I feel a single mate pair library sequence is worse than paired end at the same depth. Let me know if I am wrong.
Now, I am asked to get best out of this data. Without diving in too deep (spend too much time), what the best (practical) case scenario and the worst case scenario I should prepare the collaborator for?
I have access to a 512GB 32 core machine, and have velvet, soap denovo, and spades to use. Also a CLC bio license that can be moved to that computer. What is the recommended methods, programs, and parameters to use?
Very much appreciate your thoughts and suggestions!
By the way, I did recommend them to (at least) sequence another 50x in 2x100~150. But I don't think it is going to fly.
Thanks!!!
I am mostly comfortable with DNA resequencing, mRNAseq, ChIPseq, etc. data. And always feel difficult handling de novo assembly works. But it comes my way anyway.
I have a set of data that are mate pair sequencing of a ~1GB genome. It is close to 30x coverage after linker being removed. the insert size is about 8Kb. I don't feel it is a good idea to use mate pair only (I'd rather to have various sized libraries). Without evidence, I feel a single mate pair library sequence is worse than paired end at the same depth. Let me know if I am wrong.
Now, I am asked to get best out of this data. Without diving in too deep (spend too much time), what the best (practical) case scenario and the worst case scenario I should prepare the collaborator for?
I have access to a 512GB 32 core machine, and have velvet, soap denovo, and spades to use. Also a CLC bio license that can be moved to that computer. What is the recommended methods, programs, and parameters to use?
Very much appreciate your thoughts and suggestions!
By the way, I did recommend them to (at least) sequence another 50x in 2x100~150. But I don't think it is going to fly.
Thanks!!!
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