text: user1684: I am trying to assemble RNA virus genome using Broad Viral NGS pipeline BROAD VIRAL NGS PIPELINE. 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 ?
  
  user964: Since you are already using the Broad Tools sets you can use Picard 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
  
original_text: 1684: <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>
   964: <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>
  