assembler for viral genome sequencing data

Question

[hafiz.talhamalik]

I have raw reads of virus data. and I want to assemble the viral genome. any tool / pipeline suggestion and also help me regarding viral annotation as well

[Sej Modha]

Is it genome sequencing or metagenomic dataset? In my experience, SPAdes works well for viral genome assemblies.

[hafiz.talhamalik]

this is genome sequencing. I just tried SPAdes but not a good assembly results

[Sej Modha]

What do you mean by a not good assembly? What other pre-processing steps have you performed, e.g. adapter trimming, removing host sequences. It'd be advisable to provide as much information as possible including the sequencing platform, the type of sequencing and a bit about the samples itself. These details would help understand this specific problem better.

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[gb]

If you know which virus it is you could try to find a reference and use BWA

[GenoMax]

tadpole.sh from BBMap suite works well for small/viral genomes. A guide is available here.