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Genotyping tool for fasta sequences

Hello guys,there some tool I can genotyping my HRSV sequences in fasta format,in a fast way?

thanks in advance!!!

genome rna-seq genotyping
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updated by Ram 4.5K • | written by uirajan-kuki 3

Could you please provide more info on this, using abbreviation might not help as many people might not be aware of them!

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written by Sej Modha 528

HRSV = Human respiratory syncytial virus, in all likelihood.

uirajan-kuki : Why did you select rnaseq tag for your post? Is this RNAseq data? This is an RNA virus, so it must have been converted to DNA before sequencing (akin to RNAseq).

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written by GenoMax 16K

YES,my sequnces are converted already,now I need to genotyping them...

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written by uirajan-kuki 3

Then align them to the reference genome sequence and then call variants. Have the reads been converted to fasta format for some reason? Do you have the original fastq reads available? If so use fastq version when you do the alignments.

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written by GenoMax 16K

Congrats, if you have the dna/rna sequence of a virus in fasta format you have already genotyped it (somehow), because that is the genotype by definition. I am quite sure you meant something else, but you need to explain that better.

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written by Michael Dondrup 5.6K

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