How can I establish my own reference library for NGS data? Does somebody know an easy way to establish a tool to BLAST or compare hundreds of thousands of CO1 sequences against a reference library tool?
Thanks for the support.
In Geneious, you can create your own BLAST database in Tools -> Add/Remove Database. You need to specify the location of the BLAST binaries (available at http://blast.ncbi.nlm.nih.gov/Blast.cgi/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download) before you can setup your own database.
If you are having a large input query, and a large database, it may be faster to use the standalone version of BLAST on your own computer, or even better, on a server with multiple CPUs as Geneious tends to be slower. If your database is small, the BLAST should be relatively fast in Geneious.
Good luck!
I suggest using bowtie2 to do alignment of your ngs data to your potential reference COI sequence(s). Try my software https://github.com/rachelss/GFR and let me know if that gets you what you need.
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