Question: assembler for viral genome sequencing data
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gravatar for hafiz.talhamalik
16 months ago by
Pakistan
hafiz.talhamalik250 wrote:

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

virus assembly genome • 1.5k views
ADD COMMENTlink modified 16 months ago by Nicolas Rosewick9.3k • written 16 months ago by hafiz.talhamalik250

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

ADD REPLYlink written 16 months ago by Sej Modha4.7k

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

ADD REPLYlink written 16 months ago by hafiz.talhamalik250

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.

For more info on how to ask a good question please read: [ Please read before posting a question ] -- How To Ask A Good Question

ADD REPLYlink written 16 months ago by Sej Modha4.7k

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

ADD REPLYlink written 16 months ago by gb1.9k

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

ADD REPLYlink written 16 months ago by GenoMax95k
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