Filtering out non-target organism reads before assembly

Hello,
I have sequenced on an Illumina platform a virus grown in eggs. I want to assemble the virus genome, but the vast majority of the reads in the fastq file are not of the virus. I guess only less than 1% of the reads belong to the virus.
What tool should I use to filter all of the non-target DNA? I assume I can’t start the assembly before that.

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Hi @omer

Please see this GTN tutorial for an example. That particular protocol uses Bowtie2 to remove reads that align to the non-target genome but other mapping tools are discussed.

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