Answers.Body: <p>If you're talking RNA, I have a blog post from a while back about Diamond/MEGAN:</p>
  
  <p><a href="http://achri.blogspot.com/2017/04/data-for-free-viral-metagenomics-in.html" rel="nofollow noreferrer">http://achri.blogspot.com/2017/04/data-for-free-viral-metagenomics-in.html</a></p>
  
  <p>In principle this will work for DNA if you have a non-trivial number of pathogen reads (since they tend to be gene dense in their genomes). Otherwise I use Kraken on a database for all the NCBI nt database, but this is slower and doesn't let you sanity check the false positive taxonomy assignments as well as I describe in the post. Of course, ideally, you run multiple methods if you have the resources to do so.</p>
  
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Answers.UserDisplayName: paulgordon
Answers.Body: <p>I think you could try <a href="https://microbiomejournal.biomedcentral.com/articles/10.1186/2049-2618-2-33" rel="nofollow noreferrer">pathoscope</a> for this.</p>
  
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Answers.UserDisplayName: nsheff
Answers.Body: <p>You may find this blog post helpful: <a href="https://www.sevenbridges.com/centrifuge/" rel="nofollow noreferrer">Identifying viral sequences in TCGA data using Kraken and Centrifuge</a>.</p>
  
  <blockquote>
    <p>Our goal was to evaluate the performance of Centrifuge and Kraken for
    detecting viral transcripts across a cancer cohort. Centrifuge and
    Kraken produce very similar results and consistently detect HPV
    strains in cervical cancer.</p>
  </blockquote>
  
  <p>There is also a review <a href="https://www.frontiersin.org/articles/10.3389/fmicb.2018.00749/full" rel="nofollow noreferrer">Overview of Virus Metagenomic Classification Methods and Their Biological Applications</a>, but they focus specifically on viruses:</p>
  
  <blockquote>
    <p>We evaluated 49 published computational classification workflows for
    virus metagenomics in a literature review. To this end, we described
    the methods of existing workflows by breaking them up into five
    general steps and assessed their ease-of-use and validation
    experiments. Performance scores of previous benchmarks were summarized
    and correlations between methods and performance were investigated. We
    indicate the potential suitability of the different workflows for (1)
    time-constrained diagnostics, (2) surveillance and outbreak source
    tracing, (3) detection of remote homologies (discovery), and (4)
    biodiversity studies.</p>
  </blockquote>
  
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Answers.UserDisplayName: burger
Answers.Body: <p>To know if there are bacterial genomes in the sequenced sample I have used an approach based on kmers analysis. An useful tool to do that is <a href="https://bitbucket.org/genomicepidemiology/kmerfinder" rel="nofollow noreferrer">kmerfinder</a> which uses a kmers database built from bacterial genomes. Quoting from the kmerfinder web site: </p>
  
  <blockquote>
    <p>The method is used to find the best match (species identification) to
    the reads in one or more fastq files or one fasta file in a (kmer)
    database produced using the KMA program.</p>
  </blockquote>
  
  <p>I haven't use it for viruses genome analysis, but conceptually it should be work as well.
  Hope this would be helpful.</p>
  
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Answers.UserDisplayName: ICP
Answers.Body: <p>What type of NGS data is it? If smallRNA or RNAseq data, you can simply assemble the reads into longer contigs and do the blast search using your reference viral or bacterial sequences. </p>
  
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Answers.UserDisplayName: MAPK
Body: <p>What's the best way to test if a pair of Illumina FASTQ files from blood DNA extraction contain any reads are from viral or bacterial infection from human samples? Thanks in advance.</p>
  <p>EDIT:</p>
  <p>Looking at the available options, I started testing <a href="https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-3-r46" rel="nofollow noreferrer">Kraken</a>, the metagenomics classification (Wood and Salzberg Gen Biol 2014) for samples where I have seen an indication of viral reads. I will update with results / further questions.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-24T13:57:24.013Z
Comments.Text: There are some people voting to close this question as too broad. Perhaps you could indicate what are your requirements and what options do you consider
Comments.UserDisplayName: llrs
Tags: <fastq><ngs><covid-19>
Title: Testing for viral/bacterial infection FASTQ files
ThreadText: # Testing for viral/bacterial infection FASTQ files
  
  (Asked by: username_0 on 2019-04-17)
  
  What's the best way to test if a pair of Illumina FASTQ files from blood DNA extraction contain any reads are from viral or bacterial infection from human samples? Thanks in advance.
  
  EDIT:
  
  Looking at the available options, I started testing [Kraken](https://genomebiology.biomedcentral.com/articles/10.1186/gb-2014-15-3-r46), the metagenomics classification (Wood and Salzberg Gen Biol 2014) for samples where I have seen an indication of viral reads. I will update with results / further questions.
  
  **Tags:** fastq, ngs, covid-19
  
  > **Comments:**
  > **username_1**: There are some people voting to close this question as too broad. Perhaps you could indicate what are your requirements and what options do you consider  
  
  ---
  
  ## 5 answers
  
  ### Answer by username_2 on 2019-04-17. Score: 2
  
  If you're talking RNA, I have a blog post from a while back about Diamond/MEGAN:
  
  <http://achri.blogspot.com/2017/04/data-for-free-viral-metagenomics-in.html>
  
  In principle this will work for DNA if you have a non-trivial number of pathogen reads (since they tend to be gene dense in their genomes). Otherwise I use Kraken on a database for all the NCBI nt database, but this is slower and doesn't let you sanity check the false positive taxonomy assignments as well as I describe in the post. Of course, ideally, you run multiple methods if you have the resources to do so.
  
  
  ---
  
  ### Answer by username_3 on 2019-04-18. Score: 2
  
  I think you could try [pathoscope](https://microbiomejournal.biomedcentral.com/articles/10.1186/2049-2618-2-33) for this.
  
  
  ---
  
  ### Answer by username_4 on 2019-04-23. Score: 1
  
  You may find this blog post helpful: [Identifying viral sequences in TCGA data using Kraken and Centrifuge](https://www.sevenbridges.com/centrifuge/).
  
  > Our goal was to evaluate the performance of Centrifuge and Kraken for
  > detecting viral transcripts across a cancer cohort. Centrifuge and
  > Kraken produce very similar results and consistently detect HPV
  > strains in cervical cancer.
  
  There is also a review [Overview of Virus Metagenomic Classification Methods and Their Biological Applications](https://www.frontiersin.org/articles/10.3389/fmicb.2018.00749/full), but they focus specifically on viruses:
  
  > We evaluated 49 published computational classification workflows for
  > virus metagenomics in a literature review. To this end, we described
  > the methods of existing workflows by breaking them up into five
  > general steps and assessed their ease-of-use and validation
  > experiments. Performance scores of previous benchmarks were summarized
  > and correlations between methods and performance were investigated. We
  > indicate the potential suitability of the different workflows for (1)
  > time-constrained diagnostics, (2) surveillance and outbreak source
  > tracing, (3) detection of remote homologies (discovery), and (4)
  > biodiversity studies.
  
  
  ---
  
  ### Answer by username_5 on 2019-04-17. Score: 1
  
  To know if there are bacterial genomes in the sequenced sample I have used an approach based on kmers analysis. An useful tool to do that is [kmerfinder](https://bitbucket.org/genomicepidemiology/kmerfinder) which uses a kmers database built from bacterial genomes. Quoting from the kmerfinder web site:
  
  > The method is used to find the best match (species identification) to
  > the reads in one or more fastq files or one fasta file in a (kmer)
  > database produced using the KMA program.
  
  I haven't use it for viruses genome analysis, but conceptually it should be work as well.
  Hope this would be helpful.
  
  
  ---
  
  ### Answer by username_6 on 2019-04-18. Score: 0
  
  What type of NGS data is it? If smallRNA or RNAseq data, you can simply assemble the reads into longer contigs and do the blast search using your reference viral or bacterial sequences.
  
  
  ---
  
  