Entering edit mode
6 months ago
Mero
•
0
Hello!
I have a 900 GB eukaryotic nucleotide sequence Fasta file that I downloaded from NCBI. I want to align my query sequence (for now only one for testing purposes). For that I tried LASTZ, Nucmer, and blast.
Since I have a extremely big file LASTZ didn't work when I used sub-files more than 3GB approximately and nucmer couldn't load it and it's been killed. On the other hand, blast works fine because I am using it with blast database directly.
The thing I want to ask is: Are there any other ways such as parameters or parallelization methods that I could make use of so that LASTZ or nucmer can work faster than Blast? Or is using Blast completely utilizable in my case with even more than one query sequences?
Thank you in advance!
