Viral genome assembly using broad viral ngs pipeline? 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 ?
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