Answers.Body: <p>Since you are already using the Broad Tools sets you can use <a href="https://broadinstitute.github.io/picard/command-line-overview.html#FastqToSam" rel="nofollow noreferrer">Picard FastqToSam</a> to make the conversion</p>
  
  <p>As far a clipDb I am unfamiliar with that and a quick google search and look at the trimmomatic manual were unhelpful</p>
  
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Answers.CreationDate: 2019-04-04T01:52:32.413Z
Answers.LastActivityDate: 2019-04-04T01:52:32.413Z
Answers.UserDisplayName: Bioathlete
Body: <p>I am trying to assemble RNA virus genome using Broad Viral NGS pipeline <a href="https://viral-ngs.readthedocs.io/en/latest/assembly.html" rel="nofollow noreferrer">BROAD VIRAL NGS PIPELINE</a>. I am two questions : </p>
  
  <p>1) As this pipeline requires unaligned bam format as input, how do I convert fastq to bam ?</p>
  
  <p>2) Some of the tools like   assemble_trinity require Trimmomatic clipDb. How can I get this clipDb ?</p>
  
Tags: <genome><assembly><covid-19><sars-cov-2>
Title: Viral genome assembly using broad viral ngs pipeline?
ThreadText: # Viral genome assembly using broad viral ngs pipeline?
  
  (Asked by: username_0 on 2019-04-04)
  
  I am trying to assemble RNA virus genome using Broad Viral NGS pipeline [BROAD VIRAL NGS PIPELINE](https://viral-ngs.readthedocs.io/en/latest/assembly.html). I am two questions :
  
  1) As this pipeline requires unaligned bam format as input, how do I convert fastq to bam ?
  
  2) Some of the tools like assemble\_trinity require Trimmomatic clipDb. How can I get this clipDb ?
  
  **Tags:** genome, assembly, covid-19, sars-cov-2
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2019-04-04. Score: 4
  
  Since you are already using the Broad Tools sets you can use [Picard FastqToSam](https://broadinstitute.github.io/picard/command-line-overview.html#FastqToSam) to make the conversion
  
  As far a clipDb I am unfamiliar with that and a quick google search and look at the trimmomatic manual were unhelpful
  
  
  ---
  
  