Hi, I hope everything is fine. I have a bam file with the COVID-19 genome from the ion torrent sequencing platform. I want to assemble them and tried with spades, But there is not enough read to form a contig. In that case, I want to assemble them with having gap (NNN). Is there any tools or pipeline?
Thanks In Advance
Thank you, can you please share the code, like align with bwa and then?