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I am a Biochemist that is unfamiliar with bioinformatic tools and new to academia as a whole.

I am currently using ILLUMINA PE data, which I trimmed (Trimmomatic), corrected (Rcorrector) and assembled (SPAdes). I am now interested in using the genetic sequences from my contigs to identify the original organism (I know it is a bacterium).

I have tried using BLASTn (with default parameters) on one of my contigs. I let the query run for 30 minutes before stopping, nothing came of it.

What would be the best way to go about doing this?

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  • $\begingroup$ posted an answer here for the cross-post. biology.stackexchange.com/questions/96183/… $\endgroup$
    – Maximilian Press
    Commented Oct 6, 2020 at 20:00
  • $\begingroup$ I think the best option is using this online tool (blast.ncbi.nlm.nih.gov/Blast.cgi) If you don't have too many contigs you can just do that manually. It usually takes less than one minute even with large contigs. But if it takes too long... just use a shorter sequence and it will be as effective to find the organism. $\endgroup$
    – juanjo75es
    Commented Oct 11, 2020 at 23:35

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You can use KmerFinder and Kraken2 for taxonomy assignment

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