Answers.Body: <p>You can use <a href="https://cge.cbs.dtu.dk/services/KmerFinder/" rel="nofollow noreferrer">KmerFinder</a> and Kraken2 for taxonomy assignment</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-10-06T08:19:35.333Z
Answers.LastActivityDate: 2020-10-06T08:19:35.333Z
Answers.UserDisplayName: zorbax
Body: <p>I am a Biochemist that is unfamiliar with bioinformatic tools and new to academia as a whole.</p>
  <p>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).</p>
  <p>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.</p>
  <p>What would be the best way to go about doing this?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-10-06T20:00:37.737Z
Comments.Text: posted an answer here for the cross-post. https://biology.stackexchange.com/questions/96183/how-to-identify-an-unknown-species-from-a-fasta-file-containing-its-genome-sequ/96198#96198
Comments.UserDisplayName: Maximilian Press
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-10-11T23:35:27.887Z
Comments.Text: I think the best option is using this online tool (https://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.
Comments.UserDisplayName: juanjo75es
Tags: <fasta><blast><genomics><blastn><genetics>
Title: How to identify unknow bacterium species from whole genome genetic sequence
ThreadText: # How to identify unknow bacterium species from whole genome genetic sequence
  
  (Asked by: username_0 on 2020-10-06)
  
  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?
  
  **Tags:** fasta, blast, genomics, blastn, genetics
  
  > **Comments:**
  > **username_1**: posted an answer here for the cross-post. https://biology.stackexchange.com/questions/96183/how-to-identify-an-unknown-species-from-a-fasta-file-containing-its-genome-sequ/96198#96198  
  > **username_2**: I think the best option is using this online tool (https://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.  
  
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  ## 1 answers
  
  ### Answer by username_3 on 2020-10-06. Score: 1 | Accepted answer
  
  You can use [KmerFinder](https://cge.cbs.dtu.dk/services/KmerFinder/) and Kraken2 for taxonomy assignment
  
  
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