Gpu-Blast Vs Smalt
Hi, I am wondering if anyone has compared Smalt vs Blast. Two ways to use Smith-Waterman to map reads to a reference genome.
I recently got a hold of GPU-Blast and was wondering if it might go the same speed. If so, would it have more optimal alignments? The blast2sam.pl script would help me get the right output (forgetting about paired-end for now*), so the question boils down to 1) which is faster and 2) which has better matches. If anyone takes me up on the challenge, I think you could compare with what my computer currently has: 36 CPU threads vs 1536 GPU cores.
* followup question: is there a way to go about this while retaining paired-end-edness?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
NCBI Entrez not returning the correct DNA sequence for all entries
written by ahir29 •
-
RNA-seq normalization using housekeeping genes in EdgeR
written by k.kole •
-
Choosing Optimal Assembly from Quasta Data
written by RichelleRedekop •
-
Simple Go Analysis For Gene Expression Microarrays
written by pld
-
De Novo Assembly Using 'A5' Pipeline
written by rwn
-
Paired End Vs Single End Detection
written by Lee Katz
-
Best Way To Preprocess Barcoded Illumina Paired-End Data
written by Ying W
-
Ncbi Blast Output Missing Subject Name
written by Razzmataz •
-
What'S Faster? "Blastall -P Blastp" Or "Blastp?"
written by Lee Katz
-
Velvet: Retain Read Names In Afg File
written by Lee Katz
