How to convert genome sequencing of SARS-CoV-2 raw fastq file to consensus fasta file?

Question

[Mohamad]

Hi I am trying to generate a high-quality consensus fasta file from sequencing data of SARS-CoV-2. First, we used the vcfutils vcf2fq command line. but we can not get high-quality data due to a large number of variations in this virus. after searching about this matter, I found that we can use samtools/bcftools consensus fasta file. BUT, I think generated consensus fasta file is abnormally cleared and filtered after using cat command!! Parallelly, I use the Genome Detective tool to get the fasta file. The final lineage reports of Genome Detective and samtools/bcftools (that resulted from Pango Lineage) are totally different! would you please help me solve this problem? Is my idea about cat command correct? Is there any alternative command line to get the consensus fasta file? Thanks

[Joe]

You don't really convert FASTQ data.

It sounds like you're either asking about assembling the data, or calling variants relative to a reference, but I'm not clear on the objective here.

Answer 1

[Istvan Albert]

See a recent post on the subject

Calling a partial consensus sequence when you have low sequence coverage

[Mohamad]

Thanks, that was exactly what I needed