Dear community,
I'm planning to use Velvet to assemble a plant genome, but because I'm new to de-novo genome assembly field I have a couple of questions which I looked to resolve with no fortune at all.
The situation is that I have four different libraries:
- Nextera Mate-Pair 7Kb (HiSeq 2000) [2x101]
- Truseq Paired-end (HiSeq 2000) [2x101]
- Paired-End (MiSeq)-1 [2x300] (adapter has been trimmed, length is variable between 35-300)
- Paired-End (MiSeq)-1 [2x300] (adapter has been trimmed, length is variable between 35-300)
I was planning to perform an assembly of libs 1 and 2 within the same Velvet command (using shortPaired and shortPaired2, inspired by this blog), and then in parallel run another Velvet command of a pooled file of libs 3+4. Finally combining them-all using any other program/tool.
As a hash value I will perform runnings between 21-99 bp.
- What do you think about this strategy? Do you recommend something different?
- What do you recommend as a next step to pool down all the assemblies?
Thanks for your help!!
Sorry for being late in answering the post!
I will give it a try to this definetly!
No worries!
One word of warning about VelvetOptimiser: If you run in with several threads, the threads don't share memory. So if you have an assembly that will take 1GB in memory, and you run VelvetOptimiser with 4 threads, you will need about 4GB of memory. Try running the memory estimation function first to see how many threads you need, example from manual:
to estimate how much memory you'll need for a 4.5MB genome and 8 threads