Fastq to Fasta format

Question

[taniamahmood38]

Hello everybody,

I have fasta files and am trying them to convert to fasta format, but I am not getting the required genome size. My genome size is 8.1KB but I am getting >10KB. Can anyone please tell me the exact pipeline I should follow to convert it to fasta format?

Just for your kind information, I am using shovill assembler and I have also tried fastq - bam - fasta on galaxy software.

Thanks in advance

[rpolicastro]

Can you explain the experiment and associated details in more depth? It's hard to figure out what you're trying to do.

[taniamahmood38]

I have a virus genome in fastq format and I want it to convert to fasta format for further phylogenetic analysis. But when I try to convert that to fasta I get some 10,500 bases in the fasta file, however, the actual genome size is 8100 bases. I just want an optimized pipeline to convert from fastq to fasta. Might be, that there is some issue in trimming fastq files or removal of adapter sequences which is giving more bases than actual. But I don't know the way how to do that. If you please help me out, or if any further information is required do let me know. Thanks for your prompt response

[ATpoint]

If you have fastq (=NGS data) then the genome is sequenced, meaning chopped into pieces. For a complete genome you have into a process that is called assembly. It is not just a file format conversion, it is basically sticking the pieces (the content of the fastq) together to form a genome.

[taniamahmood38]

Thanks for your guidance. I have used the shovill de novo genome assembler tool, but I am not getting the required genome size. Is there any other way to do that?