assembler for viral genome sequencing data
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
• 3,200 views
•
link
updated
by
Nicolas Rosewick
•
written
by
hafiz.talhamalik
•
written
by
hafiz.talhamalik
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How to quantify the viral sequencing reads from RNA-seq data?
written by Huy Duong •
-
Plant Genome Annotation
written by hafiz.talhamalik
-
Whole Metagenome Analysis of resistome dataset
written by hafiz.talhamalik
-
Viral Genome Denovo Assembly
written by hafiz.talhamalik
-
technique to assemble mitochondria from whole genome
written by hafiz.talhamalik
-
de novo annotation of plants genome
written by hafiz.talhamalik
-
How to assemble viral genomes when my data contains host DNA as well
written by GBC_Zonatos •
-
SNPS finding for bacterial sequences
written by hafiz.talhamalik
-
Viral Whole genome Deep Sequencing within Human Host
written by Clark_BioMorgan •
-
Method To Identify Viral Integration Site In Human Genome From Ngs Data?
written by Obi Griffith
Is it genome sequencing or metagenomic dataset? In my experience, SPAdes works well for viral genome assemblies.
this is genome sequencing. I just tried SPAdes but not a good assembly results
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
If you know which virus it is you could try to find a reference and use BWA
tadpole.shfrom BBMap suite works well for small/viral genomes. A guide is available here.