I need to design primers for around 40,000 sequences. After doing this task with Primer3, I found that it took a very long time.
I I tried to accelerate primer3 operation with GNU parallel, but I cannot managed to successfully use GNU parallel to split input file and do multi-thread operation. Somehow primer3 still ran on 1 core only.
My command is as the following:
cat fasta.p3in | parallel --round-robin -j 12 --pipe --recend "=" /Tools/primer3/primer3-2.3.6/src/primer3_core > fasta.p3out
Could anyone tell the correct way to use GNU Parallel along with Primer3? Thanks a lot!