@@ -16,7 +16,8 @@ I thought of the Knuth Morris Pratt algorithm which I found implemented in the t
...
@@ -16,7 +16,8 @@ I thought of the Knuth Morris Pratt algorithm which I found implemented in the t
Here are the results of the tests with the different implementation.
Here are the results of the tests with the different implementation.
For the tests, I used the files in the data-virome directory.
For the tests, I used the files in the data-virome directory.
My aim was to bench execution time and to see how openCL or another python package could improve things compared to regexp. So, I didn' bother with Pair-end. I searched for the first 20 characters (default value for seed in phageterm) of each SRR4295172_1_div6.fastq in all the sequences in Contigs_30min.fasta.
My aim was to bench execution time and to see how openCL or another python package could improve things compared to regexp. So, I didn' bother with Pair-end. I searched for the first 20 characters (default value for seed in phageterm) of each SRR4295172_1_div6.fastq in all the sequences in Contigs_30min.fasta.
Tests ran on myriad-n403 or on my machine (openCL part).
