Question: Parallelly assemble Illumina shortreads using velvet assembler
0
gravatar for Vivek bagaria
4.4 years ago by
Stanford
Vivek bagaria0 wrote:

I am using velvet assembler to assemble the human genome of the cell line 12877. I ran velveth using the command - velveth output 25 Homo_sapiens_assembly18.fasta . Since my .fasta file is huge, I wanted to parallelize the above process.

My attempt

I have tried the following commands

  1. make 'OPENMP=1'
  2. export OMP_NUM_THREADS=8
  3. export OMP_THREAD_LIMIT=8
  4. velveth output 25 Homo_sapiens_assembly18.fasta

There seems to be no change in running time, after trying the above commands. Am I missing anything? Could someone help me with this?

sequencing assembly • 1.1k views
ADD COMMENTlink modified 4.4 years ago by Antonio R. Franco4.5k • written 4.4 years ago by Vivek bagaria0
0
gravatar for Antonio R. Franco
4.4 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.5k wrote:

Not all parts of Velvet run in parallel. You don't mention what command have you tested, whether is velveth or velvetg, but with a "make 'OPENMP=1'

  • You surely compile the program to run in parallel
  • Is not needed to define anumber of threads in this program in the command lane. It will automatically use all threads available without you writting anything else
  • You will notice is running in parallel because at the time of generating the roadmap, numbers of proccessed reads don't come to the screen in order. They will appear in sets by the order the thread is running
ADD COMMENTlink written 4.4 years ago by Antonio R. Franco4.5k
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