<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>

CC BY-SA 4.0
2019-04-04T01:52:32.413Z
2019-04-04T01:52:32.413Z
Bioathlete
<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>

<genome><assembly><covid-19><sars-cov-2>
Viral genome assembly using broad viral ngs pipeline?
# 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


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