... | ... | @@ -16,7 +16,8 @@ I thought of the Knuth Morris Pratt algorithm which I found implemented in the t |
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Here are the results of the tests with the different implementation.
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For the tests, I used the files in the data-virome directory.
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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.
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Tests ran on myriad-n403 or on my machine (openCL part).
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| original regexp | tryalgo | openCL |
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| --------------- |:---------:| ------:|
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| | >24hours | 120s | |
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| 17min10s | >24hours | 30s | |