vsearch instead of usearch?

[tseemann]

usearch is not open source can you replace it with vsearch? https://github.com/torognes/vsearch

[Xiaojun928]

It is much faster after replacing usearch with vsearch with multi threads. Thanks for your suggestions @tseemann. The modification can be done for the usearch_multi.py from line 26 to 39.

Here is the updated code:

 #run usearch
                args = []
                args.append(USEARCH_PATH)
                args.append('--usearch_global')
                args.append(path + sp + '/genes/' + prot1)
                args.append('--db')
                args.append(path + sp + '/genes/'  + prot2)
                args.append('--id')
                args.append('0.7')
                args.append('--threads')
                args.append('32')  ## This can be changed based on your dataset
                args.append('--strand')
                args.append('plus')
                args.append('--blast6out')